diff --git a/app/Models/Application.php b/app/Models/Application.php
index fd7f486b9..3905281d8 100644
--- a/app/Models/Application.php
+++ b/app/Models/Application.php
@@ -1279,15 +1279,19 @@ public function dirOnServer()
         return application_configuration_dir()."/{$this->uuid}";
     }
 
-    public function setGitImportSettings(string $deployment_uuid, string $git_clone_command, bool $public = false, ?string $commit = null, ?string $git_ssh_command = null)
+    public function setGitImportSettings(string $deployment_uuid, string $git_clone_command, bool $public = false, ?string $commit = null, ?string $gitSshCommand = null, ?string $git_ssh_command = null, ?string $gitConfigOptions = null)
     {
         $baseDir = $this->generateBaseDir($deployment_uuid);
         $escapedBaseDir = escapeshellarg($baseDir);
         $isShallowCloneEnabled = $this->settings?->is_git_shallow_clone_enabled ?? false;
+        $gitCommand = $gitConfigOptions ? "git {$gitConfigOptions}" : 'git';
 
-        // Use the full GIT_SSH_COMMAND (including -i for SSH key and port options) when provided,
-        // so that git fetch, submodule update, and lfs pull can authenticate the same way as git clone.
-        $sshCommand = $git_ssh_command ?? 'GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"';
+        $resolvedGitSshCommand = $git_ssh_command ?? $gitSshCommand;
+        $sshCommand = $resolvedGitSshCommand
+            ? (str_starts_with($resolvedGitSshCommand, 'GIT_SSH_COMMAND=')
+                ? $resolvedGitSshCommand
+                : 'GIT_SSH_COMMAND="'.$resolvedGitSshCommand.'"')
+            : 'GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"';
 
         // Use the explicitly passed commit (e.g. from rollback), falling back to the application's git_commit_sha.
         // Invalid refs will cause the git checkout/fetch command to fail on the remote server.
@@ -1298,9 +1302,9 @@ public function setGitImportSettings(string $deployment_uuid, string $git_clone_
             // If shallow clone is enabled and we need a specific commit,
             // we need to fetch that specific commit with depth=1
             if ($isShallowCloneEnabled) {
-                $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} git fetch --depth=1 origin {$escapedCommit} && git -c advice.detachedHead=false checkout {$escapedCommit} >/dev/null 2>&1";
+                $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} {$gitCommand} fetch --depth=1 origin {$escapedCommit} && {$gitCommand} -c advice.detachedHead=false checkout {$escapedCommit} >/dev/null 2>&1";
             } else {
-                $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} git -c advice.detachedHead=false checkout {$escapedCommit} >/dev/null 2>&1";
+                $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} {$gitCommand} -c advice.detachedHead=false checkout {$escapedCommit} >/dev/null 2>&1";
             }
         }
         if ($this->settings->is_git_submodules_enabled) {
@@ -1311,10 +1315,10 @@ public function setGitImportSettings(string $deployment_uuid, string $git_clone_
             }
             // Add shallow submodules flag if shallow clone is enabled
             $submoduleFlags = $isShallowCloneEnabled ? '--depth=1' : '';
-            $git_clone_command = "{$git_clone_command} git submodule sync && {$sshCommand} git submodule update --init --recursive {$submoduleFlags}; fi";
+            $git_clone_command = "{$git_clone_command} {$gitCommand} submodule sync && {$sshCommand} {$gitCommand} submodule update --init --recursive {$submoduleFlags}; fi";
         }
         if ($this->settings->is_git_lfs_enabled) {
-            $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} git lfs pull";
+            $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$sshCommand} {$gitCommand} lfs pull";
         }
 
         return $git_clone_command;
@@ -1555,6 +1559,11 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                 } else {
                     $github_access_token = generateGithubInstallationToken($this->source);
                     $encodedToken = rawurlencode($github_access_token);
+
+                    // Rewrite same-host HTTPS URLs only for these git commands so submodules can authenticate without persisting credentials.
+                    $gitConfigOption = '-c '.escapeshellarg("url.{$source_html_url_scheme}://x-access-token:{$encodedToken}@{$source_html_url_host}/.insteadOf={$source_html_url_scheme}://{$source_html_url_host}/");
+                    $git_clone_command = str_replace('git clone', "git {$gitConfigOption} clone", $git_clone_command);
+
                     if ($exec_in_docker) {
                         $repoUrl = "$source_html_url_scheme://x-access-token:$encodedToken@$source_html_url_host/{$customRepository}.git";
                         $escapedRepoUrl = escapeshellarg($repoUrl);
@@ -1567,7 +1576,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                         $fullRepoUrl = $repoUrl;
                     }
                     if (! $only_checkout) {
-                        $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command, public: false, commit: $commit);
+                        $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command, public: false, commit: $commit, gitConfigOptions: $gitConfigOption);
                     }
                     if ($exec_in_docker) {
                         $commands->push(executeInDocker($deployment_uuid, $git_clone_command));
@@ -1578,7 +1587,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                 if ($pull_request_id !== 0) {
                     $branch = "pull/{$pull_request_id}/head:$pr_branch_name";
 
-                    $git_checkout_command = $this->buildGitCheckoutCommand($pr_branch_name);
+                    $git_checkout_command = $this->buildGitCheckoutCommand($pr_branch_name, gitConfigOptions: $gitConfigOption ?? null);
                     $escapedPrBranch = escapeshellarg($branch);
                     if ($exec_in_docker) {
                         $commands->push(executeInDocker($deployment_uuid, "cd {$escapedBaseDir} && git fetch origin {$escapedPrBranch} && $git_checkout_command"));
@@ -1603,12 +1612,13 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                     $private_key = base64_encode($private_key);
                     $gitlabPort = $gitlabSource->custom_port ?? 22;
                     $escapedCustomRepository = escapeshellarg($customRepository);
-                    $gitlabSshCommand = "GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$gitlabPort} -o Port={$gitlabPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\"";
-                    $git_clone_command_base = "{$gitlabSshCommand} {$git_clone_command} {$escapedCustomRepository} {$escapedBaseDir}";
+                    $gitlabSshCommand = "ssh -o ConnectTimeout=30 -p {$gitlabPort} -o Port={$gitlabPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa";
+                    $gitlabGitSshCommand = "GIT_SSH_COMMAND=\"{$gitlabSshCommand}\"";
+                    $git_clone_command_base = "{$gitlabGitSshCommand} {$git_clone_command} {$escapedCustomRepository} {$escapedBaseDir}";
                     if ($only_checkout) {
                         $git_clone_command = $git_clone_command_base;
                     } else {
-                        $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command_base, commit: $commit, git_ssh_command: $gitlabSshCommand);
+                        $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command_base, commit: $commit, gitSshCommand: $gitlabSshCommand);
                     }
                     if ($exec_in_docker) {
                         $commands = collect([
@@ -1631,7 +1641,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                         } else {
                             $commands->push("echo 'Checking out $branch'");
                         }
-                        $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$gitlabPort} -o Port={$gitlabPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name);
+                        $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && {$gitlabGitSshCommand} git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name, $gitlabSshCommand);
                     }
 
                     if ($exec_in_docker) {
@@ -1674,12 +1684,13 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
             }
             $private_key = base64_encode($private_key);
             $escapedCustomRepository = escapeshellarg($customRepository);
-            $deployKeySshCommand = "GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\"";
-            $git_clone_command_base = "{$deployKeySshCommand} {$git_clone_command} {$escapedCustomRepository} {$escapedBaseDir}";
+            $deployKeySshCommand = "ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa";
+            $deployKeyGitSshCommand = "GIT_SSH_COMMAND=\"{$deployKeySshCommand}\"";
+            $git_clone_command_base = "{$deployKeyGitSshCommand} {$git_clone_command} {$escapedCustomRepository} {$escapedBaseDir}";
             if ($only_checkout) {
                 $git_clone_command = $git_clone_command_base;
             } else {
-                $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command_base, commit: $commit, git_ssh_command: $deployKeySshCommand);
+                $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command_base, commit: $commit, gitSshCommand: $deployKeySshCommand);
             }
             if ($exec_in_docker) {
                 $commands = collect([
@@ -1702,7 +1713,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$deployKeySshCommand}\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name, $deployKeySshCommand);
                 } elseif ($git_type === 'github' || $git_type === 'gitea') {
                     $branch = "pull/{$pull_request_id}/head:$pr_branch_name";
                     if ($exec_in_docker) {
@@ -1710,14 +1721,14 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$deployKeySshCommand}\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name, $deployKeySshCommand);
                 } elseif ($git_type === 'bitbucket') {
                     if ($exec_in_docker) {
                         $commands->push(executeInDocker($deployment_uuid, "echo 'Checking out $branch'"));
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" ".$this->buildGitCheckoutCommand($commit);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$deployKeySshCommand}\" ".$this->buildGitCheckoutCommand($commit, $deployKeySshCommand);
                 }
             }
 
@@ -1738,6 +1749,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
             $escapedCustomRepository = escapeshellarg($customRepository);
             $git_clone_command = "{$git_clone_command} {$escapedCustomRepository} {$escapedBaseDir}";
             $git_clone_command = $this->setGitImportSettings($deployment_uuid, $git_clone_command, public: true, commit: $commit);
+            $otherSshCommand = "ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa";
 
             if ($pull_request_id !== 0) {
                 if ($git_type === 'gitlab') {
@@ -1747,7 +1759,7 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$otherSshCommand}\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name, $otherSshCommand);
                 } elseif ($git_type === 'github' || $git_type === 'gitea') {
                     $branch = "pull/{$pull_request_id}/head:$pr_branch_name";
                     if ($exec_in_docker) {
@@ -1755,14 +1767,14 @@ public function generateGitImportCommands(string $deployment_uuid, int $pull_req
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$otherSshCommand}\" git fetch origin $branch && ".$this->buildGitCheckoutCommand($pr_branch_name, $otherSshCommand);
                 } elseif ($git_type === 'bitbucket') {
                     if ($exec_in_docker) {
                         $commands->push(executeInDocker($deployment_uuid, "echo 'Checking out $branch'"));
                     } else {
                         $commands->push("echo 'Checking out $branch'");
                     }
-                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"ssh -o ConnectTimeout=30 -p {$customPort} -o Port={$customPort} -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa\" ".$this->buildGitCheckoutCommand($commit);
+                    $git_clone_command = "{$git_clone_command} && cd {$escapedBaseDir} && GIT_SSH_COMMAND=\"{$otherSshCommand}\" ".$this->buildGitCheckoutCommand($commit, $otherSshCommand);
                 }
             }
 
@@ -2011,13 +2023,15 @@ public function fqdns(): Attribute
         );
     }
 
-    protected function buildGitCheckoutCommand($target): string
+    protected function buildGitCheckoutCommand($target, ?string $gitSshCommand = null, ?string $gitConfigOptions = null): string
     {
         $escapedTarget = escapeshellarg($target);
-        $command = "git checkout {$escapedTarget}";
+        $gitCommand = $gitConfigOptions ? "git {$gitConfigOptions}" : 'git';
+        $command = "{$gitCommand} checkout {$escapedTarget}";
 
         if ($this->settings->is_git_submodules_enabled) {
-            $command .= ' && git submodule update --init --recursive';
+            $sshCommand = $gitSshCommand ?? 'ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null';
+            $command .= " && GIT_SSH_COMMAND=\"{$sshCommand}\" {$gitCommand} submodule update --init --recursive";
         }
 
         return $command;
diff --git a/bootstrap/helpers/api.php b/bootstrap/helpers/api.php
index 8088e6b99..4b76200d2 100644
--- a/bootstrap/helpers/api.php
+++ b/bootstrap/helpers/api.php
@@ -144,7 +144,7 @@ function sharedDataApplications()
         'docker_compose_custom_start_command' => \App\Support\ValidationPatterns::shellSafeCommandRules(),
         'docker_compose_custom_build_command' => \App\Support\ValidationPatterns::shellSafeCommandRules(),
         'is_container_label_escape_enabled' => 'boolean',
-        'is_preserve_repository_enabled' => 'boolean'
+        'is_preserve_repository_enabled' => 'boolean',
     ];
 }
 
diff --git a/bootstrap/helpers/proxy.php b/bootstrap/helpers/proxy.php
index ed18dfe76..d443c84a4 100644
--- a/bootstrap/helpers/proxy.php
+++ b/bootstrap/helpers/proxy.php
@@ -110,6 +110,7 @@ function connectProxyToNetworks(Server $server)
     if ($server->isSwarm()) {
         $commands = $networks->map(function ($network) {
             $safe = escapeshellarg($network);
+
             return [
                 "docker network ls --format '{{.Name}}' | grep '^{$network}$' >/dev/null || docker network create --driver overlay --attachable {$safe} >/dev/null",
                 "docker network connect {$safe} coolify-proxy >/dev/null 2>&1 || true",
@@ -119,6 +120,7 @@ function connectProxyToNetworks(Server $server)
     } else {
         $commands = $networks->map(function ($network) {
             $safe = escapeshellarg($network);
+
             return [
                 "docker network ls --format '{{.Name}}' | grep '^{$network}$' >/dev/null || docker network create --attachable {$safe} >/dev/null",
                 "docker network connect {$safe} coolify-proxy >/dev/null 2>&1 || true",
@@ -144,6 +146,7 @@ function ensureProxyNetworksExist(Server $server)
     if ($server->isSwarm()) {
         $commands = $networks->map(function ($network) {
             $safe = escapeshellarg($network);
+
             return [
                 "echo 'Ensuring network {$safe} exists...'",
                 "docker network ls --format '{{.Name}}' | grep -q '^{$network}$' || docker network create --driver overlay --attachable {$safe}",
@@ -152,6 +155,7 @@ function ensureProxyNetworksExist(Server $server)
     } else {
         $commands = $networks->map(function ($network) {
             $safe = escapeshellarg($network);
+
             return [
                 "echo 'Ensuring network {$safe} exists...'",
                 "docker network ls --format '{{.Name}}' | grep -q '^{$network}$' || docker network create --attachable {$safe}",
diff --git a/tests/Unit/GitHubAppSubmoduleCredentialsTest.php b/tests/Unit/GitHubAppSubmoduleCredentialsTest.php
new file mode 100644
index 000000000..48f18d2a5
--- /dev/null
+++ b/tests/Unit/GitHubAppSubmoduleCredentialsTest.php
@@ -0,0 +1,49 @@
+<?php
+
+namespace App\Models {
+    function generateGithubInstallationToken(GithubApp $source): string
+    {
+        return 'review token/with+symbols';
+    }
+}
+
+namespace {
+    use App\Models\Application;
+    use App\Models\ApplicationSetting;
+    use App\Models\GithubApp;
+
+    test('private github app submodule credentials use per command git config', function () {
+        $application = new Application;
+        $application->forceFill([
+            'uuid' => 'test-app-uuid',
+            'git_repository' => 'coollabsio/private-app',
+            'git_branch' => 'main',
+            'git_commit_sha' => 'HEAD',
+        ]);
+
+        $settings = new ApplicationSetting;
+        $settings->is_git_shallow_clone_enabled = false;
+        $settings->is_git_submodules_enabled = true;
+        $settings->is_git_lfs_enabled = false;
+        $application->setRelation('settings', $settings);
+
+        $source = new GithubApp;
+        $source->forceFill([
+            'html_url' => 'https://github.com',
+            'api_url' => 'https://api.github.com',
+            'is_public' => false,
+        ]);
+        $application->setRelation('source', $source);
+
+        $result = $application->generateGitImportCommands(
+            deployment_uuid: 'test-deployment',
+            exec_in_docker: false,
+        );
+
+        expect($result['commands'])
+            ->not->toContain('git config --global')
+            ->toContain("git -c 'url.https://x-access-token:review%20token%2Fwith%2Bsymbols@github.com/.insteadOf=https://github.com/' clone --recurse-submodules -b 'main'")
+            ->toContain("git -c 'url.https://x-access-token:review%20token%2Fwith%2Bsymbols@github.com/.insteadOf=https://github.com/' submodule sync")
+            ->toContain("git -c 'url.https://x-access-token:review%20token%2Fwith%2Bsymbols@github.com/.insteadOf=https://github.com/' submodule update --init --recursive");
+    });
+}
diff --git a/tests/Unit/GitSubmoduleCredentialTest.php b/tests/Unit/GitSubmoduleCredentialTest.php
new file mode 100644
index 000000000..5ac5c501a
--- /dev/null
+++ b/tests/Unit/GitSubmoduleCredentialTest.php
@@ -0,0 +1,168 @@
+<?php
+
+use App\Models\Application;
+use App\Models\ApplicationSetting;
+use App\Models\GitlabApp;
+use App\Models\PrivateKey;
+
+describe('Git submodule credential propagation', function () {
+    beforeEach(function () {
+        $this->application = new Application;
+        $this->application->forceFill([
+            'uuid' => 'test-app-uuid',
+            'git_commit_sha' => 'HEAD',
+        ]);
+
+        $settings = new ApplicationSetting;
+        $settings->is_git_shallow_clone_enabled = false;
+        $settings->is_git_submodules_enabled = true;
+        $settings->is_git_lfs_enabled = false;
+        $this->application->setRelation('settings', $settings);
+    });
+
+    test('setGitImportSettings uses provided gitSshCommand for submodule update', function () {
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -o Port=22 -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa';
+
+        $result = $this->application->setGitImportSettings(
+            deployment_uuid: 'test-uuid',
+            git_clone_command: 'git clone',
+            public: false,
+            gitSshCommand: $sshCommand
+        );
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git submodule update --init --recursive')
+            ->toContain('git submodule sync');
+    });
+
+    test('setGitImportSettings uses default ssh command when no gitSshCommand provided', function () {
+        $result = $this->application->setGitImportSettings(
+            deployment_uuid: 'test-uuid',
+            git_clone_command: 'git clone',
+            public: false,
+        );
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" git submodule update --init --recursive');
+    });
+
+    test('setGitImportSettings uses provided gitSshCommand for fetch and checkout', function () {
+        $this->application->git_commit_sha = 'abc123def456';
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -o Port=22 -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa';
+
+        $result = $this->application->setGitImportSettings(
+            deployment_uuid: 'test-uuid',
+            git_clone_command: 'git clone',
+            public: false,
+            gitSshCommand: $sshCommand
+        );
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git -c advice.detachedHead=false checkout');
+    });
+
+    test('setGitImportSettings uses provided gitSshCommand for shallow fetch', function () {
+        $this->application->git_commit_sha = 'abc123def456';
+        $this->application->settings->is_git_shallow_clone_enabled = true;
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -o Port=22 -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa';
+
+        $result = $this->application->setGitImportSettings(
+            deployment_uuid: 'test-uuid',
+            git_clone_command: 'git clone',
+            public: false,
+            gitSshCommand: $sshCommand
+        );
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git fetch --depth=1 origin');
+    });
+
+    test('setGitImportSettings uses provided gitSshCommand for lfs pull', function () {
+        $this->application->settings->is_git_lfs_enabled = true;
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -i /root/.ssh/id_rsa';
+
+        $result = $this->application->setGitImportSettings(
+            deployment_uuid: 'test-uuid',
+            git_clone_command: 'git clone',
+            public: false,
+            gitSshCommand: $sshCommand
+        );
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git lfs pull');
+    });
+
+    test('buildGitCheckoutCommand includes GIT_SSH_COMMAND for submodule update when provided', function () {
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -i /root/.ssh/id_rsa';
+
+        $method = new ReflectionMethod($this->application, 'buildGitCheckoutCommand');
+        $result = $method->invoke($this->application, 'main', $sshCommand);
+
+        expect($result)
+            ->toContain("git checkout 'main'")
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git submodule update --init --recursive');
+    });
+
+    test('buildGitCheckoutCommand uses default ssh command for submodule update when none provided', function () {
+        $method = new ReflectionMethod($this->application, 'buildGitCheckoutCommand');
+        $result = $method->invoke($this->application, 'main');
+
+        expect($result)
+            ->toContain('GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" git submodule update --init --recursive');
+    });
+
+    test('buildGitCheckoutCommand omits submodule update when submodules disabled', function () {
+        $this->application->settings->is_git_submodules_enabled = false;
+
+        $method = new ReflectionMethod($this->application, 'buildGitCheckoutCommand');
+        $result = $method->invoke($this->application, 'main');
+
+        expect($result)
+            ->toContain("git checkout 'main'")
+            ->not->toContain('submodule');
+    });
+
+    test('generateGitImportCommands uses GitLab private key for PR submodule checkout', function () {
+        $settings = new ApplicationSetting;
+        $settings->is_git_shallow_clone_enabled = false;
+        $settings->is_git_submodules_enabled = true;
+        $settings->is_git_lfs_enabled = false;
+
+        $privateKey = Mockery::mock(PrivateKey::class)->makePartial();
+        $privateKey->shouldReceive('getAttribute')->with('private_key')->andReturn('fake-private-key');
+
+        $gitlabSource = Mockery::mock(GitlabApp::class)->makePartial();
+        $gitlabSource->shouldReceive('getMorphClass')->andReturn(GitlabApp::class);
+        $gitlabSource->shouldReceive('getAttribute')->with('privateKey')->andReturn($privateKey);
+        $gitlabSource->shouldReceive('getAttribute')->with('custom_port')->andReturn(22);
+        $gitlabSource->shouldReceive('getAttribute')->with('html_url')->andReturn('https://gitlab.com');
+
+        $application = Mockery::mock(Application::class)->makePartial();
+        $application->git_branch = 'main';
+        $application->git_commit_sha = 'HEAD';
+        $application->setRelation('settings', $settings);
+        $application->source = $gitlabSource;
+        $application->shouldReceive('deploymentType')->andReturn('source');
+        $application->shouldReceive('customRepository')->andReturn([
+            'repository' => 'git@gitlab.com:user/repo.git',
+            'port' => 22,
+        ]);
+        $application->shouldReceive('getAttribute')->with('source')->andReturn($gitlabSource);
+
+        $result = $application->generateGitImportCommands(
+            deployment_uuid: 'test-uuid',
+            pull_request_id: 123,
+            git_type: 'gitlab',
+            exec_in_docker: false,
+        );
+
+        $sshCommand = 'ssh -o ConnectTimeout=30 -p 22 -o Port=22 -o LogLevel=ERROR -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /root/.ssh/id_rsa';
+
+        expect($result['commands'])
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git fetch origin merge-requests/123/head:pr-123-coolify')
+            ->toContain("git checkout 'pr-123-coolify'")
+            ->toContain('GIT_SSH_COMMAND="'.$sshCommand.'" git submodule update --init --recursive')
+            ->not->toContain('GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" git submodule update --init --recursive');
+    });
+
+});
diff --git a/tests/Unit/ProxyConfigRecoveryTest.php b/tests/Unit/ProxyConfigRecoveryTest.php
index e10d899fe..682407bdf 100644
--- a/tests/Unit/ProxyConfigRecoveryTest.php
+++ b/tests/Unit/ProxyConfigRecoveryTest.php
@@ -163,7 +163,7 @@ function mockServerWithDbConfig(?string $savedConfig, string $proxyType = 'TRAEF
 });
 
 it('accepts stored config when YAML parsing fails', function () {
-    $invalidYaml = "this: is: not: [valid yaml: {{{}}}";
+    $invalidYaml = 'this: is: not: [valid yaml: {{{}}}';
     $server = mockServerWithDbConfig($invalidYaml, 'TRAEFIK');
 
     // Invalid YAML should not block — configMatchesProxyType returns true on parse failure