diff --git a/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveClassCleaner.java b/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveClassCleaner.java
new file mode 100644
--- /dev/null
+++ b/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveClassCleaner.java
@@ -0,0 +1,137 @@
+/*
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ *
+ * Copyright 2012 Oracle and/or its affiliates. All rights reserved.
+ *
+ * Oracle and Java are registered trademarks of Oracle and/or its affiliates.
+ * Other names may be trademarks of their respective owners.
+ *
+ * The contents of this file are subject to the terms of either the GNU
+ * General Public License Version 2 only ("GPL") or the Common
+ * Development and Distribution License("CDDL") (collectively, the
+ * "License"). You may not use this file except in compliance with the
+ * License. You can obtain a copy of the License at
+ * http://www.netbeans.org/cddl-gplv2.html
+ * or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
+ * specific language governing permissions and limitations under the
+ * License.  When distributing the software, include this License Header
+ * Notice in each file and include the License file at
+ * nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the GPL Version 2 section of the License file that
+ * accompanied this code. If applicable, add the following below the
+ * License Header, with the fields enclosed by brackets [] replaced by
+ * your own identifying information:
+ * "Portions Copyrighted [year] [name of copyright owner]"
+ *
+ * If you wish your version of this file to be governed by only the CDDL
+ * or only the GPL Version 2, indicate your decision by adding
+ * "[Contributor] elects to include this software in this distribution
+ * under the [CDDL or GPL Version 2] license." If you do not indicate a
+ * single choice of license, a recipient has the option to distribute
+ * your version of this file under either the CDDL, the GPL Version 2 or
+ * to extend the choice of license to its licensees as provided above.
+ * However, if you add GPL Version 2 code and therefore, elected the GPL
+ * Version 2 license, then the option applies only if the new code is
+ * made subject to such option by the copyright holder.
+ *
+ * Contributor(s):
+ *
+ * Portions Copyrighted 2012 Sun Microsystems, Inc.
+ */
+
+package org.netbeans.modules.maven.groovy;
+
+import java.io.IOException;
+import org.netbeans.api.project.Project;
+import org.netbeans.api.project.ProjectUtils;
+import org.netbeans.api.project.SourceGroup;
+import org.netbeans.modules.groovy.support.api.GroovySources;
+import org.netbeans.modules.maven.spi.cos.CompileOnSaveClassCleaner;
+import org.netbeans.spi.project.ProjectServiceProvider;
+import org.openide.filesystems.FileObject;
+import org.openide.util.Exceptions;
+
+/**
+ *
+ * @author Martin Janicek
+ */
+@ProjectServiceProvider(
+    projectType = "org-netbeans-modules-maven",
+    service = CompileOnSaveClassCleaner.class
+)
+public class GroovyCompileOnSaveClassCleaner implements CompileOnSaveClassCleaner {
+
+    @Override
+    public void clean(Project project, boolean testDir) {
+        if (project.getProjectDirectory() == null) {
+            return;
+        }
+
+        final FileObject targetClasses;
+        if (testDir) {
+            targetClasses = project.getProjectDirectory().getFileObject("target/test-classes"); //NOI18N
+        } else {
+            targetClasses = project.getProjectDirectory().getFileObject("target/classes"); //NOI18N
+        }
+
+        for (SourceGroup sourceGroup : GroovySources.getGroovySourceGroups(ProjectUtils.getSources(project))) {
+            cleanSourceRoot(targetClasses, sourceGroup.getRootFolder(), testDir);
+        }
+    }
+
+    private void cleanSourceRoot(FileObject targetClasses, FileObject sourceRoot, boolean testRoot) {
+        if (testRoot) {
+            // We want to clean test directories only
+            if (sourceRoot.getPath().endsWith("/src/test/groovy") || sourceRoot.getPath().endsWith("/src/test/java")) { //NOI18N
+                cleanClassFiles(targetClasses, sourceRoot, sourceRoot);
+            }
+        } else {
+            // We want to clean source directories only
+            if (sourceRoot.getPath().endsWith("/src/main/groovy") || sourceRoot.getPath().endsWith("/src/main/java")) { //NOI18N
+                cleanClassFiles(targetClasses, sourceRoot, sourceRoot);
+            }
+        }
+    }
+
+    private void cleanClassFiles(FileObject targetClasses, FileObject rootFolder, FileObject folder) {
+        for (FileObject child : folder.getChildren()) {
+            if (child.isFolder()) {
+                cleanClassFiles(targetClasses, rootFolder, child);
+            } else {
+                deleteClassFile(targetClasses, rootFolder, child);
+            }
+        }
+    }
+
+    private void deleteClassFile(FileObject targetClasses, FileObject rootFolder, FileObject sourceFile) {
+        final String sourceFilePath = sourceFile.getPath();
+
+        // Do not delete anything different than class files for groovy files!
+        if (!sourceFilePath.endsWith(".groovy")) { //NOI18N
+            return;
+        }
+
+        // We are trying to get location of the same file (only with .class extension instead of .groovy)
+        // but in target/classes --> need to strip everything related to the source folder
+        //
+        // Instead of "/tmp/MavenApplication1/src/main/groovy/packagename/subpackage/SomeGroovyFile.groovy"
+        // we will get only "packagename/subpackage/SomeGroovyFile.groovy"
+
+        final int indexOfFQN = rootFolder.getPath().length() + 1;
+        final String sourceFileFQN = sourceFilePath.substring(indexOfFQN);
+
+        // Just changing the extension from "groovy" to "class"
+        final String classFilePath = sourceFileFQN.substring(0, sourceFileFQN.length() - 6) + "class"; //NOI18N
+
+        // ..and finally finding the file in target/classes folder
+        final FileObject classFile = targetClasses.getFileObject(classFilePath); //NOI18N
+        if (classFile != null) {
+            try {
+                classFile.delete();
+            } catch (IOException ex) {
+                Exceptions.printStackTrace(ex);
+            }
+        }
+    }
+}
diff --git a/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveSkipper.java b/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveSkipper.java
new file mode 100644
--- /dev/null
+++ b/maven.groovy/src/org/netbeans/modules/maven/groovy/GroovyCompileOnSaveSkipper.java
@@ -0,0 +1,65 @@
+/*
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ *
+ * Copyright 2012 Oracle and/or its affiliates. All rights reserved.
+ *
+ * Oracle and Java are registered trademarks of Oracle and/or its affiliates.
+ * Other names may be trademarks of their respective owners.
+ *
+ * The contents of this file are subject to the terms of either the GNU
+ * General Public License Version 2 only ("GPL") or the Common
+ * Development and Distribution License("CDDL") (collectively, the
+ * "License"). You may not use this file except in compliance with the
+ * License. You can obtain a copy of the License at
+ * http://www.netbeans.org/cddl-gplv2.html
+ * or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
+ * specific language governing permissions and limitations under the
+ * License.  When distributing the software, include this License Header
+ * Notice in each file and include the License file at
+ * nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the GPL Version 2 section of the License file that
+ * accompanied this code. If applicable, add the following below the
+ * License Header, with the fields enclosed by brackets [] replaced by
+ * your own identifying information:
+ * "Portions Copyrighted [year] [name of copyright owner]"
+ *
+ * If you wish your version of this file to be governed by only the CDDL
+ * or only the GPL Version 2, indicate your decision by adding
+ * "[Contributor] elects to include this software in this distribution
+ * under the [CDDL or GPL Version 2] license." If you do not indicate a
+ * single choice of license, a recipient has the option to distribute
+ * your version of this file under either the CDDL, the GPL Version 2 or
+ * to extend the choice of license to its licensees as provided above.
+ * However, if you add GPL Version 2 code and therefore, elected the GPL
+ * Version 2 license, then the option applies only if the new code is
+ * made subject to such option by the copyright holder.
+ *
+ * Contributor(s):
+ *
+ * Portions Copyrighted 2012 Sun Microsystems, Inc.
+ */
+
+package org.netbeans.modules.maven.groovy;
+
+import org.netbeans.modules.maven.api.execute.RunConfig;
+import org.netbeans.modules.maven.spi.cos.CompileOnSaveSkipper;
+import org.openide.filesystems.FileObject;
+
+/**
+ *
+ * @author Martin Janicek
+ */
+@org.openide.util.lookup.ServiceProvider(service=CompileOnSaveSkipper.class)
+public class GroovyCompileOnSaveSkipper implements CompileOnSaveSkipper {
+
+    @Override
+    public boolean skip(RunConfig config, boolean includingTests, long timeStamp) {
+        final FileObject runFile = config.getSelectedFileObject();
+
+        if ("groovy".equals(runFile.getExt())) { //NOI18N
+            return true;
+        }
+        return false;
+    }
+}
diff --git a/maven/manifest.mf b/maven/manifest.mf
--- a/maven/manifest.mf
+++ b/maven/manifest.mf
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 OpenIDE-Module: org.netbeans.modules.maven/2
-OpenIDE-Module-Specification-Version: 2.61
+OpenIDE-Module-Specification-Version: 2.62
 OpenIDE-Module-Localizing-Bundle: org/netbeans/modules/maven/Bundle.properties
 OpenIDE-Module-Layer: org/netbeans/modules/maven/layer.xml
 AutoUpdate-Show-In-Client: false
diff --git a/maven/src/org/netbeans/modules/maven/cos/CosChecker.java b/maven/src/org/netbeans/modules/maven/cos/CosChecker.java
--- a/maven/src/org/netbeans/modules/maven/cos/CosChecker.java
+++ b/maven/src/org/netbeans/modules/maven/cos/CosChecker.java
@@ -85,6 +85,7 @@
 import org.netbeans.modules.maven.customizer.CustomizerProviderImpl;
 import org.netbeans.modules.maven.customizer.RunJarPanel;
 import org.netbeans.modules.maven.execute.DefaultReplaceTokenProvider;
+import org.netbeans.modules.maven.spi.cos.CompileOnSaveClassCleaner;
 import org.netbeans.modules.maven.spi.cos.CompileOnSaveSkipper;
 import org.netbeans.spi.java.classpath.support.ClassPathSupport;
 import org.netbeans.spi.project.ActionProvider;
@@ -774,6 +775,10 @@
             MavenProject mvn = prj.getMavenProject();
             if (RunUtils.hasApplicationCompileOnSaveEnabled(project)) {
                 touchCoSTimeStamp(mvn, false);
+
+                for (CompileOnSaveClassCleaner cleaner : project.getLookup().lookupAll(CompileOnSaveClassCleaner.class)) {
+                    cleaner.clean(project, false);
+                }
             } else {
                 File f = getCoSFile(mvn, false);
                 boolean doClean = f != null && f.exists();
@@ -788,6 +793,10 @@
             }
             if (RunUtils.hasTestCompileOnSaveEnabled(project)) {
                 touchCoSTimeStamp(mvn, true);
+
+                for (CompileOnSaveClassCleaner cleaner : project.getLookup().lookupAll(CompileOnSaveClassCleaner.class)) {
+                    cleaner.clean(project, true);
+                }
             } else {
                 deleteCoSTimeStamp(mvn, true);
             }
diff --git a/maven/src/org/netbeans/modules/maven/spi/cos/CompileOnSaveClassCleaner.java b/maven/src/org/netbeans/modules/maven/spi/cos/CompileOnSaveClassCleaner.java
new file mode 100644
--- /dev/null
+++ b/maven/src/org/netbeans/modules/maven/spi/cos/CompileOnSaveClassCleaner.java
@@ -0,0 +1,68 @@
+/*
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ *
+ * Copyright 2012 Oracle and/or its affiliates. All rights reserved.
+ *
+ * Oracle and Java are registered trademarks of Oracle and/or its affiliates.
+ * Other names may be trademarks of their respective owners.
+ *
+ * The contents of this file are subject to the terms of either the GNU
+ * General Public License Version 2 only ("GPL") or the Common
+ * Development and Distribution License("CDDL") (collectively, the
+ * "License"). You may not use this file except in compliance with the
+ * License. You can obtain a copy of the License at
+ * http://www.netbeans.org/cddl-gplv2.html
+ * or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
+ * specific language governing permissions and limitations under the
+ * License.  When distributing the software, include this License Header
+ * Notice in each file and include the License file at
+ * nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the GPL Version 2 section of the License file that
+ * accompanied this code. If applicable, add the following below the
+ * License Header, with the fields enclosed by brackets [] replaced by
+ * your own identifying information:
+ * "Portions Copyrighted [year] [name of copyright owner]"
+ *
+ * If you wish your version of this file to be governed by only the CDDL
+ * or only the GPL Version 2, indicate your decision by adding
+ * "[Contributor] elects to include this software in this distribution
+ * under the [CDDL or GPL Version 2] license." If you do not indicate a
+ * single choice of license, a recipient has the option to distribute
+ * your version of this file under either the CDDL, the GPL Version 2 or
+ * to extend the choice of license to its licensees as provided above.
+ * However, if you add GPL Version 2 code and therefore, elected the GPL
+ * Version 2 license, then the option applies only if the new code is
+ * made subject to such option by the copyright holder.
+ *
+ * Contributor(s):
+ *
+ * Portions Copyrighted 2012 Sun Microsystems, Inc.
+ */
+
+package org.netbeans.modules.maven.spi.cos;
+
+import org.netbeans.api.project.Project;
+
+/**
+ * Enables to clean some class files even if the Compile on Save feature is enabled.
+ *
+ * Normally if the Compile on Save feature is enabled, class files aren't deleted
+ * when running application. Because of that they are not recompiled as the maven
+ * runner thinks they are already up to date. This is not desirable in a certain
+ * situations (e.g. we don't have CoS implemented for groovy files and thus we want
+ * to recompile their class files even if CoS is enabled).
+ *
+ * @author Martin Janicek
+ * @since 2.62
+ */
+public interface CompileOnSaveClassCleaner {
+
+    /**
+     *
+     * @param project current project
+     * @param testDir true if the we want to clean test directory, false if we
+     * want to clean source directory
+     */
+    void clean(Project project, boolean testDir);
+}