diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
index 707117d25cd1..3d7b7c89e5c0 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
@@ -506,7 +506,7 @@ public class IncProjectBuilder {
         SourceToOutputMappingImpl mapping = null;
         try {
           mapping = myProjectDescriptor.dataManager.createSourceToOutputMapForStaleTarget(type, stringId);
-          clearOutputFiles(context, mapping, type);
+          clearOutputFiles(context, mapping, type, ids.second);
         }
         finally {
           if (mapping != null) {
@@ -526,13 +526,17 @@ public class IncProjectBuilder {
   public static void clearOutputFiles(CompileContext context, BuildTarget<?> target) throws IOException {
     final SourceToOutputMapping map = context.getProjectDescriptor().dataManager.getSourceToOutputMap(target);
     BuildTargetType<?> targetType = target.getTargetType();
-    clearOutputFiles(context, map, targetType);
+    clearOutputFiles(context, map, targetType, context.getProjectDescriptor().dataManager.getTargetsState().getBuildTargetId(target));
     registerTargetsWithClearedOutput(context, Collections.singletonList(target));
   }
 
-  private static void clearOutputFiles(CompileContext context, SourceToOutputMapping mapping, BuildTargetType<?> targetType) throws IOException {
+  private static void clearOutputFiles(CompileContext context,
+                                       SourceToOutputMapping mapping,
+                                       BuildTargetType<?> targetType,
+                                       int targetId) throws IOException {
     final THashSet<File> dirsToDelete = targetType instanceof ModuleBasedBuildTargetType<?>
                                         ? new THashSet<>(FileUtil.FILE_HASHING_STRATEGY) : null;
+    OutputToTargetRegistry outputToTargetRegistry = context.getProjectDescriptor().dataManager.getOutputToTargetRegistry();
     for (String srcPath : mapping.getSources()) {
       final Collection<String> outs = mapping.getOutputs(srcPath);
       if (outs != null && !outs.isEmpty()) {
@@ -540,6 +544,7 @@ public class IncProjectBuilder {
         for (String out : outs) {
           BuildOperations.deleteRecursively(out, deletedPaths, dirsToDelete);
         }
+        outputToTargetRegistry.removeMapping(outs, targetId);
         if (!deletedPaths.isEmpty()) {
           context.processMessage(new FileDeletedEvent(deletedPaths));
         }
diff --git a/jps/jps-builders/testSrc/org/jetbrains/jps/builders/CleanStaleTargetsTest.kt b/jps/jps-builders/testSrc/org/jetbrains/jps/builders/CleanStaleTargetsTest.kt
index 59e3be06a13a..ba93df1af0a5 100644
--- a/jps/jps-builders/testSrc/org/jetbrains/jps/builders/CleanStaleTargetsTest.kt
+++ b/jps/jps-builders/testSrc/org/jetbrains/jps/builders/CleanStaleTargetsTest.kt
@@ -9,7 +9,8 @@ import org.jetbrains.jps.util.JpsPathUtil
 
 class CleanStaleTargetsTest : JpsBuildTestCase() {
   fun `test delete old output when module is deleted`() {
-    doTestDeleteOldOutput {
+    //todo[nik, jeka] currently references to classes from deleted module aren't removed ClassToSubclasses, ClassToClassDependency, SourceFileToClasses mappings
+    doTestDeleteOldOutput(false) {
       myProject.removeModule(it)
     }
   }
@@ -28,7 +29,7 @@ class CleanStaleTargetsTest : JpsBuildTestCase() {
     }
   }
 
-  private fun doTestDeleteOldOutput(action: (JpsModule) -> Unit) {
+  private fun doTestDeleteOldOutput(checkMappings: Boolean = true, action: (JpsModule) -> Unit) {
     JpsJavaExtensionService.getInstance().getOrCreateProjectExtension(myProject).outputUrl = JpsPathUtil.pathToUrl(getAbsolutePath("out"))
     val aRoot = PathUtil.getParentPath(createFile("a/src/A.java", "class A {}"))
     val aModule = addModule("a", arrayOf(aRoot), null, null, jdk)
@@ -44,10 +45,14 @@ class CleanStaleTargetsTest : JpsBuildTestCase() {
     //do not clean output when just one other target is built to avoid unexpectedly long builds
     assertOutput(aOutput.absolutePath, directoryContent { file("A.class") })
 
-    buildAllModules()
+    val buildResult = buildAllModules()
     //clean output of stale targets when all targets of this type are built
     if (aOutput.exists()) {
       assertOutput(aOutput.absolutePath, directoryContent { })
     }
+
+    if (checkMappings) {
+      checkMappingsAreSameAfterRebuild(buildResult)
+    }
   }
 }