diff --git a/src/Application/ApplicationFileProcessor.php b/src/Application/ApplicationFileProcessor.php
index 6cfd9b99bb6..09a9b1e7b73 100644
--- a/src/Application/ApplicationFileProcessor.php
+++ b/src/Application/ApplicationFileProcessor.php
@@ -56,6 +56,9 @@ public function __construct(
 
     public function run(Configuration $configuration, InputInterface $input): ProcessResult
     {
+        // scope the cache to this run's --only / --only-suffix selection before any cache read/write
+        $this->changedFilesDetector->setActiveScope($configuration->getOnlyRule(), $configuration->getOnlySuffix());
+
         $filePaths = $this->filesFinder->findFilesInPaths($configuration->getPaths(), $configuration);
 
         // no files found
@@ -121,6 +124,9 @@ public function processFiles(
         ?callable $preFileCallback = null,
         ?callable $postFileCallback = null
     ): ProcessResult {
+        // also set here: parallel workers reach processFiles() via WorkerCommand, bypassing run()
+        $this->changedFilesDetector->setActiveScope($configuration->getOnlyRule(), $configuration->getOnlySuffix());
+
         /** @var SystemError[] $systemErrors */
         $systemErrors = [];
 
@@ -179,11 +185,8 @@ private function processFile(File $file, Configuration $configuration): FileProc
         if ($fileProcessResult->getSystemErrors() !== []) {
             $this->changedFilesDetector->invalidateFile($file->getFilePath());
         } elseif (! $configuration->isDryRun() || ! $fileProcessResult->getFileDiff() instanceof FileDiff) {
-            // a file clean under a subset of rules is not necessarily clean under all rules,
-            // caching it would hide its pending changes from the next full run
-            if ($configuration->getOnlyRule() === null && $configuration->getOnlySuffix() === null) {
-                $this->changedFilesDetector->cacheFile($file->getFilePath());
-            }
+            // selective runs are safe to cache now — the key is scoped to the rule selection
+            $this->changedFilesDetector->cacheFile($file->getFilePath());
         }
 
         return $fileProcessResult;
diff --git a/src/Caching/Detector/ChangedFilesDetector.php b/src/Caching/Detector/ChangedFilesDetector.php
index 46718bab661..93bc528806f 100644
--- a/src/Caching/Detector/ChangedFilesDetector.php
+++ b/src/Caching/Detector/ChangedFilesDetector.php
@@ -21,6 +21,9 @@ final class ChangedFilesDetector
      */
     private array $cacheableFiles = [];
 
+    // scopes the per-file cache key to the active --only / --only-suffix selection (empty = full run)
+    private string $scopeSuffix = '';
+
     public function __construct(
         private readonly FileHashComputer $fileHashComputer,
         private readonly Cache $cache,
@@ -28,6 +31,14 @@ public function __construct(
     ) {
     }
 
+    public function setActiveScope(?string $onlyRule, ?string $onlySuffix): void
+    {
+        // each selection gets its own cache key, so --only and full runs coexist without clearing or poisoning
+        $this->scopeSuffix = ($onlyRule === null && $onlySuffix === null)
+            ? ''
+            : '|only:' . ($onlyRule ?? '') . '|suffix:' . ($onlySuffix ?? '');
+    }
+
     public function cacheFile(string $filePath): void
     {
         $filePathCacheKey = $this->getFilePathCacheKey($filePath);
@@ -95,7 +106,7 @@ private function resolvePath(string $filePath): string
 
     private function getFilePathCacheKey(string $filePath): string
     {
-        return $this->fileHasher->hash($this->resolvePath($filePath));
+        return $this->fileHasher->hash($this->resolvePath($filePath) . $this->scopeSuffix);
     }
 
     private function hashFile(string $filePath): string
diff --git a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
index 09c75c0c246..286a9b64ef9 100644
--- a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
+++ b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
@@ -38,7 +38,7 @@ public function testCleanFileIsCachedAsUnchanged(): void
         $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
     }
 
-    public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
+    public function testOnlyRuleRunCachesUnderOwnScopeWithoutPoisoningFullRun(): void
     {
         $filePath = __DIR__ . '/Source/CleanFile.php';
 
@@ -47,11 +47,16 @@ public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
             onlyRule: RemoveEmptyClassMethodRector::class
         ));
 
-        // a file clean under one rule is not necessarily clean under all rules
+        // a repeated --only run hits its own scoped cache entry
+        $this->changedFilesDetector->setActiveScope(RemoveEmptyClassMethodRector::class, null);
+        $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
+
+        // a full run uses a different scope key, so it is not poisoned
+        $this->changedFilesDetector->setActiveScope(null, null);
         $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
     }
 
-    public function testOnlySuffixRunDoesNotCacheFileAsUnchanged(): void
+    public function testOnlySuffixRunCachesUnderOwnScopeWithoutPoisoningFullRun(): void
     {
         $filePath = __DIR__ . '/Source/CleanFile.php';
 
@@ -60,6 +65,10 @@ public function testOnlySuffixRunDoesNotCacheFileAsUnchanged(): void
             onlySuffix: 'Controller.php'
         ));
 
+        $this->changedFilesDetector->setActiveScope(null, 'Controller.php');
+        $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
+
+        $this->changedFilesDetector->setActiveScope(null, null);
         $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
     }
 }