diff --git a/.github/workflows/mt.yaml b/.github/workflows/mt.yaml
index a3c1726ff..a5d988456 100644
--- a/.github/workflows/mt.yaml
+++ b/.github/workflows/mt.yaml
@@ -11,7 +11,7 @@ on:
       - master
 
 env:
-  MIN_MSI: 71.39
+  MIN_MSI: 71.35
   MIN_COVERED_MSI: 86.78
 
 jobs:
diff --git a/src/Configuration/ConfigurationFactory.php b/src/Configuration/ConfigurationFactory.php
index 71cdf62c8..57e59058d 100644
--- a/src/Configuration/ConfigurationFactory.php
+++ b/src/Configuration/ConfigurationFactory.php
@@ -151,7 +151,7 @@ public function create(
                 $schema->getSource()->getDirectories(),
                 $schema->getSource()->getExcludes()
             ),
-            $this->retrieveFilter($filter, $gitDiffFilter, $isForGitDiffLines, $gitDiffBase),
+            $this->retrieveFilter($filter, $gitDiffFilter, $isForGitDiffLines, $gitDiffBase, $schema->getSource()->getDirectories()),
             $schema->getSource()->getExcludes(),
             $this->retrieveLogs($schema->getLogs(), $useGitHubLogger, $htmlLogFilePath),
             $logVerbosity,
@@ -303,7 +303,10 @@ private function retrieveIgnoreSourceCodeMutatorsMap(array $resolvedMutatorsMap)
         return $map;
     }
 
-    private function retrieveFilter(string $filter, ?string $gitDiffFilter, bool $isForGitDiffLines, ?string $gitDiffBase): string
+    /**
+     * @param string[] $sourceDirectories
+     */
+    private function retrieveFilter(string $filter, ?string $gitDiffFilter, bool $isForGitDiffLines, ?string $gitDiffBase, array $sourceDirectories): string
     {
         if ($gitDiffFilter === null && !$isForGitDiffLines) {
             return $filter;
@@ -312,10 +315,10 @@ private function retrieveFilter(string $filter, ?string $gitDiffFilter, bool $is
         $baseBranch = $gitDiffBase ?? GitDiffFileProvider::DEFAULT_BASE;
 
         if ($isForGitDiffLines) {
-            return $this->gitDiffFileProvider->provide('AM', $baseBranch);
+            return $this->gitDiffFileProvider->provide('AM', $baseBranch, $sourceDirectories);
         }
 
-        return $this->gitDiffFileProvider->provide($gitDiffFilter, $baseBranch);
+        return $this->gitDiffFileProvider->provide($gitDiffFilter, $baseBranch, $sourceDirectories);
     }
 
     private function retrieveLogs(Logs $logs, ?bool $useGitHubLogger, ?string $htmlLogFilePath): Logs
diff --git a/src/Logger/GitHub/GitDiffFileProvider.php b/src/Logger/GitHub/GitDiffFileProvider.php
index 608e0d961..ab8a92aac 100644
--- a/src/Logger/GitHub/GitDiffFileProvider.php
+++ b/src/Logger/GitHub/GitDiffFileProvider.php
@@ -35,7 +35,9 @@
 
 namespace Infection\Logger\GitHub;
 
+use function array_map;
 use function escapeshellarg;
+use function implode;
 use Infection\Process\ShellCommandLineExecutor;
 use function Safe\sprintf;
 use Symfony\Component\Process\Exception\ProcessFailedException;
@@ -54,14 +56,18 @@ public function __construct(private ShellCommandLineExecutor $shellCommandLineEx
     {
     }
 
-    public function provide(string $gitDiffFilter, string $gitDiffBase): string
+    /**
+     * @param string[] $sourceDirectories
+     */
+    public function provide(string $gitDiffFilter, string $gitDiffBase, array $sourceDirectories): string
     {
         $referenceCommit = $this->findReferenceCommit($gitDiffBase);
 
         $filter = $this->shellCommandLineExecutor->execute(sprintf(
-            'git diff %s --diff-filter=%s --name-only | grep src/ | paste -s -d "," -',
+            'git diff %s --diff-filter=%s --name-only -- %s | paste -s -d "," -',
             escapeshellarg($referenceCommit),
-            escapeshellarg($gitDiffFilter)
+            escapeshellarg($gitDiffFilter),
+            implode(' ', array_map('\\escapeshellarg', $sourceDirectories))
         ));
 
         if ($filter === '') {
diff --git a/tests/phpunit/Logger/GitHub/GitDiffFileProviderTest.php b/tests/phpunit/Logger/GitHub/GitDiffFileProviderTest.php
index e993e3ee7..3e7890fe4 100644
--- a/tests/phpunit/Logger/GitHub/GitDiffFileProviderTest.php
+++ b/tests/phpunit/Logger/GitHub/GitDiffFileProviderTest.php
@@ -53,17 +53,17 @@ public function test_it_throws_no_code_to_mutate_exception_when_diff_is_empty():
         $this->expectException(NoFilesInDiffToMutate::class);
 
         $diffProvider = new GitDiffFileProvider($shellCommandLineExecutor);
-        $diffProvider->provide('AM', 'master');
+        $diffProvider->provide('AM', 'master', ['src/']);
     }
 
     public function test_it_executes_diff_and_returns_filter_as_a_string(): void
     {
         $expectedMergeBaseCommandLine = 'git merge-base \'master\' HEAD';
-        $expectedDiffCommandLine = 'git diff \'0ABCMERGE_BASE_342\' --diff-filter=\'AM\' --name-only | grep src/ | paste -s -d "," -';
+        $expectedDiffCommandLine = 'git diff \'0ABCMERGE_BASE_342\' --diff-filter=\'AM\' --name-only -- \'app/\' \'my lib/\' | paste -s -d "," -';
 
         if (PHP_OS_FAMILY === 'Windows') {
             $expectedMergeBaseCommandLine = 'git merge-base "master" HEAD';
-            $expectedDiffCommandLine = 'git diff "0ABCMERGE_BASE_342" --diff-filter="AM" --name-only | grep src/ | paste -s -d "," -';
+            $expectedDiffCommandLine = 'git diff "0ABCMERGE_BASE_342" --diff-filter="AM" --name-only -- "app/" "my lib/" | paste -s -d "," -';
         }
 
         $shellCommandLineExecutor = $this->createMock(ShellCommandLineExecutor::class);
@@ -75,16 +75,16 @@ public function test_it_executes_diff_and_returns_filter_as_a_string(): void
                     case $expectedMergeBaseCommandLine:
                         return "0ABCMERGE_BASE_342\n";
                     case $expectedDiffCommandLine:
-                        return 'src/A.php,src/B.php';
+                        return 'app/A.php,my lib/B.php';
                     default:
                         $this->fail("Unexpected shell command: $command");
                 }
             });
 
         $diffProvider = new GitDiffFileProvider($shellCommandLineExecutor);
-        $filter = $diffProvider->provide('AM', 'master');
+        $filter = $diffProvider->provide('AM', 'master', ['app/', 'my lib/']);
 
-        $this->assertSame('src/A.php,src/B.php', $filter);
+        $this->assertSame('app/A.php,my lib/B.php', $filter);
     }
 
     public function test_it_provides_lines_filter_as_a_string(): void