diff --git a/src/Application/ApplicationFileProcessor.php b/src/Application/ApplicationFileProcessor.php
index 932593d032f..98f75c0d14e 100644
--- a/src/Application/ApplicationFileProcessor.php
+++ b/src/Application/ApplicationFileProcessor.php
@@ -173,7 +173,11 @@ private function processFile(File $file, Configuration $configuration): FileProc
         if ($fileProcessResult->getSystemErrors() !== []) {
             $this->changedFilesDetector->invalidateFile($file->getFilePath());
         } elseif (! $configuration->isDryRun() || ! $fileProcessResult->getFileDiff() instanceof FileDiff) {
-            $this->changedFilesDetector->cacheFile($file->getFilePath());
+            // 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());
+            }
         }
 
         return $fileProcessResult;
diff --git a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
new file mode 100644
index 00000000000..09c75c0c246
--- /dev/null
+++ b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
@@ -0,0 +1,65 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Rector\Tests\Application\ApplicationFileProcessor;
+
+use Rector\Application\ApplicationFileProcessor;
+use Rector\Caching\Detector\ChangedFilesDetector;
+use Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector;
+use Rector\Testing\PHPUnit\AbstractLazyTestCase;
+use Rector\ValueObject\Configuration;
+
+final class ApplicationFileProcessorTest extends AbstractLazyTestCase
+{
+    private ApplicationFileProcessor $applicationFileProcessor;
+
+    private ChangedFilesDetector $changedFilesDetector;
+
+    protected function setUp(): void
+    {
+        parent::setUp();
+
+        $this->applicationFileProcessor = $this->make(ApplicationFileProcessor::class);
+        $this->changedFilesDetector = $this->make(ChangedFilesDetector::class);
+    }
+
+    protected function tearDown(): void
+    {
+        $this->changedFilesDetector->clear();
+    }
+
+    public function testCleanFileIsCachedAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/CleanFile.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(isDryRun: true));
+
+        $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+
+    public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/CleanFile.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
+            isDryRun: true,
+            onlyRule: RemoveEmptyClassMethodRector::class
+        ));
+
+        // a file clean under one rule is not necessarily clean under all rules
+        $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+
+    public function testOnlySuffixRunDoesNotCacheFileAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/CleanFile.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
+            isDryRun: true,
+            onlySuffix: 'Controller.php'
+        ));
+
+        $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+}
diff --git a/tests/Application/ApplicationFileProcessor/Source/CleanFile.php b/tests/Application/ApplicationFileProcessor/Source/CleanFile.php
new file mode 100644
index 00000000000..4dce24c580d
--- /dev/null
+++ b/tests/Application/ApplicationFileProcessor/Source/CleanFile.php
@@ -0,0 +1,13 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Rector\Tests\Application\ApplicationFileProcessor\Source;
+
+final class CleanFile
+{
+    public function run(): string
+    {
+        return 'nothing to change';
+    }
+}