diff --git a/README.md b/README.md
index d95ae27..79dff5d 100644
--- a/README.md
+++ b/README.md
@@ -146,7 +146,7 @@ The ``ec`` binary supports the following options:
 | ``--uncovered``            | ``-u``   | Lists all files which are not covered by .editorconfig.                                                                                                                             |
 | ``--verbose``              | ``-v``   | Shows additional informations, like detailed info about internal time tracking and which binary files have been skipped.                                                            |
 | ``--no-interaction``       | ``-n``   | Do not ask for confirmation, if more than 500 files found and continue scanning.                                                                                                    |
-| ``--no-error-on-exit``     |          | By default ``ec`` returns code 2 when issues occurred. With this option set return code is always 0.                                                                                |
+| ``--no-error-on-exit``     |          | By default ``ec`` returns code 2 when issues or code 1 when warnings occurred. With this option set return code is always 0.                                                        |
 
 **Tip:** The "usage" section on ``ec``'s help page shows some examples.
 
diff --git a/src/Application.php b/src/Application.php
index cc6ce83..609bb88 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -193,6 +193,22 @@ protected function executing(Input $input, Output $output): int
             ? $this->scan($finder, $count, $io, (bool)$input->getOption('strict'), (bool)$input->getOption('no-progress'), (bool)$input->getOption('compact'), (bool)$input->getOption('uncovered'))
             : $this->fix($finder, $io, (bool)$input->getOption('strict'));
 
+        if (!empty($this->scanner->getUnavailableFiles())) {
+            $amountUnavailableFiles = count($this->scanner->getUnavailableFiles());
+            $io->warning('Found ' . $amountUnavailableFiles . ' unavailable ' . StringFormatUtility::pluralizeFiles($amountUnavailableFiles) . ' not being scanned!');
+            $filePaths = [];
+            foreach ($this->scanner->getUnavailableFiles() as $unavailableFile) {
+                $filePaths[] = $unavailableFile->getPathname();
+            }
+            $io->listing($filePaths);
+            if ($gitOnlyEnabled) {
+                $io->writeln('<comment>The files listed by the "' . $gitOnlyCommand . '" command are not physically present.</comment>');
+                $io->writeln('<comment>This typically occurs when files are deleted without being staged in Git. To verify, check "git status".</comment>');
+                $io->newLine();
+            }
+            $returnValue = 1;
+        }
+
         if ($this->isVerbose) {
             if (!empty($this->scanner->getSkippedBinaryFiles())) {
                 $amountBinaryFiles = count($this->scanner->getSkippedBinaryFiles());
diff --git a/src/EditorConfig/Rules/FileUnavailableException.php b/src/EditorConfig/Rules/FileUnavailableException.php
new file mode 100644
index 0000000..d1808a7
--- /dev/null
+++ b/src/EditorConfig/Rules/FileUnavailableException.php
@@ -0,0 +1,24 @@
+<?php
+
+declare(strict_types = 1);
+
+namespace Armin\EditorconfigCli\EditorConfig\Rules;
+
+use Symfony\Component\Finder\SplFileInfo;
+
+class FileUnavailableException extends \Exception
+{
+    private SplFileInfo $unavailableFile;
+
+    public function getUnavailableFile(): SplFileInfo
+    {
+        return $this->unavailableFile;
+    }
+
+    public function setUnavailableFile(SplFileInfo $unavailableFile): self
+    {
+        $this->unavailableFile = $unavailableFile;
+
+        return $this;
+    }
+}
diff --git a/src/EditorConfig/Rules/Validator.php b/src/EditorConfig/Rules/Validator.php
index 42d3ba1..a84830d 100644
--- a/src/EditorConfig/Rules/Validator.php
+++ b/src/EditorConfig/Rules/Validator.php
@@ -34,6 +34,11 @@ public function createValidatedFileResult(SplFileInfo $file, array $editorConfig
         $this->skippingRules = $skippingRules;
 
         $filePath = (string)$file->getRealPath();
+
+        if (empty($filePath)) {
+            throw (new FileUnavailableException())->setUnavailableFile($file);
+        }
+
         $rules = [];
 
         if (!MimeTypeUtility::isCommonTextType($filePath) && (MimeTypeUtility::isCommonBinaryType($filePath) || MimeTypeUtility::isBinaryFileType($filePath))) {
diff --git a/src/EditorConfig/Scanner.php b/src/EditorConfig/Scanner.php
index 327bfce..741b3ab 100644
--- a/src/EditorConfig/Scanner.php
+++ b/src/EditorConfig/Scanner.php
@@ -5,11 +5,13 @@
 namespace Armin\EditorconfigCli\EditorConfig;
 
 use Armin\EditorconfigCli\EditorConfig\Rules\FileResult;
+use Armin\EditorconfigCli\EditorConfig\Rules\FileUnavailableException;
 use Armin\EditorconfigCli\EditorConfig\Rules\Validator;
 use Armin\EditorconfigCli\EditorConfig\Utility\MimeTypeUtility;
 use Armin\EditorconfigCli\EditorConfig\Utility\TimeTrackingUtility;
 use Idiosyncratic\EditorConfig\EditorConfig;
 use Symfony\Component\Finder\Finder;
+use Symfony\Component\Finder\SplFileInfo;
 
 class Scanner
 {
@@ -38,6 +40,11 @@ class Scanner
      */
     private $skippedBinaryFiles = [];
 
+    /**
+     * @var array|SplFileInfo[]
+     */
+    private $unavailableFiles = [];
+
     public function __construct(?EditorConfig $editorConfig = null, ?Validator $validator = null, string $rootPath = null, array $skippingRules = [])
     {
         $this->editorConfig = $editorConfig ?? new EditorConfig();
@@ -71,6 +78,14 @@ public function getSkippedBinaryFiles(): array
         return $this->skippedBinaryFiles;
     }
 
+    /**
+     * @return array|SplFileInfo[]
+     */
+    public function getUnavailableFiles(): array
+    {
+        return $this->unavailableFiles;
+    }
+
     /**
      * @param bool $strict when true, any difference of indention size is spotted
      *
@@ -82,7 +97,13 @@ public function scan(Finder $finderInstance, bool $strict = false, callable $tic
         foreach ($finderInstance as $file) {
             $config = $this->editorConfig->getConfigForPath((string)$file->getRealPath());
 
-            $fileResult = $this->validator->createValidatedFileResult($file, $config, $strict, $this->skippingRules);
+            try {
+                $fileResult = $this->validator->createValidatedFileResult($file, $config, $strict, $this->skippingRules);
+            } catch (FileUnavailableException $e) {
+                $this->unavailableFiles[] = $e->getUnavailableFile();
+                continue;
+            }
+
             $filePath = $fileResult->getFilePath();
             if (!empty($this->rootPath)) {
                 $filePath = substr($filePath, strlen($this->rootPath));
diff --git a/tests/Functional/EditorConfig/CommandGitUnavailableFilesTest.php b/tests/Functional/EditorConfig/CommandGitUnavailableFilesTest.php
new file mode 100644
index 0000000..7f412f0
--- /dev/null
+++ b/tests/Functional/EditorConfig/CommandGitUnavailableFilesTest.php
@@ -0,0 +1,58 @@
+<?php declare(strict_types = 1);
+namespace Armin\EditorconfigCli\Tests\Functional\EditorConfig;
+
+use Armin\EditorconfigCli\Application;
+use Symfony\Component\Console\Tester\CommandTester;
+
+class CommandGitUnavailableFilesTest extends AbstractTestCase
+{
+    private const GIT_BINARY = 'git';
+
+    protected $editorConfig = <<<TXT
+root = true
+
+[*]
+insert_final_newline = true
+
+TXT;
+
+    public function setUp(): void
+    {
+        $this->workspacePath = sys_get_temp_dir() . '/current_editorconfig_cli_test';
+
+        parent::setUp();
+
+        // Copy test files
+        copy(__DIR__ . '/../../Fixtures/image.jpg', $this->workspacePath . '/' . 'image.jpg');
+        copy(__DIR__ . '/../../Fixtures/document.pdf', $this->workspacePath . '/' . 'document.pdf');
+        copy(__DIR__ . '/../../Fixtures/kreis-weiß.svg', $this->workspacePath . '/' . 'kreis-weiß.svg');
+
+        // Set up Git repository for testing
+        exec('cd ' . $this->workspacePath . ' && ' . self::GIT_BINARY . ' init', $result, $returnCode);
+        if ($returnCode !== 0) {
+            throw new \RuntimeException('Unable to create test git repository!');
+        }
+
+        // Add files to git stage
+        exec('cd ' . $this->workspacePath . ' && ' . self::GIT_BINARY . ' add image.jpg');
+        exec('cd ' . $this->workspacePath . ' && ' . self::GIT_BINARY . ' add document.pdf');
+        exec('cd ' . $this->workspacePath . ' && ' . self::GIT_BINARY . ' add kreis-weiß.svg');
+
+        // Remove files physically
+        exec('rm -f ' . $this->workspacePath . '/image.jpg');
+        exec('rm -f ' . $this->workspacePath . '/document.pdf');
+    }
+
+    public function testUnavailableFiles()
+    {
+        $command = new Application();
+        $command->setAutoExit(false);
+        $commandTester = new CommandTester($command);
+        $commandTester->execute(['-d' => $this->workspacePath, '--no-progress' => true, '--git-only' => true]);
+
+        self::assertSame(1, $commandTester->getStatusCode());
+        self::assertStringContainsString('[WARNING] Found 2 unavailable files not being scanned!', $commandTester->getDisplay());
+        self::assertStringContainsString('* ' . $this->workspacePath . '/document.pdf', $commandTester->getDisplay());
+        self::assertStringContainsString('* ' . $this->workspacePath . '/image.jpg', $commandTester->getDisplay());
+    }
+}