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
@@ -47,6 +47,7 @@
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -58,6 +59,7 @@
 import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
+import java.util.TreeSet;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.maven.model.Build;
@@ -71,6 +73,8 @@
 import org.netbeans.modules.maven.api.execute.PrerequisitesChecker;
 import org.netbeans.modules.maven.api.execute.RunConfig;
 import org.netbeans.api.java.project.runner.JavaRunner;
+import org.netbeans.api.java.queries.BinaryForSourceQuery;
+import org.netbeans.api.java.queries.SourceForBinaryQuery;
 import org.netbeans.api.project.Project;
 import org.netbeans.api.project.ProjectUtils;
 import org.netbeans.api.project.SourceGroup;
@@ -565,8 +569,37 @@
                 executePaths.add(cp);
             }
         }
+        ClassPath exec = ClassPathSupport.createProxyClassPath(executePaths.toArray(new ClassPath[executePaths.size()]));
+        Set<File> toClean = new TreeSet<File>();
+        for (ClassPath.Entry entry : exec.entries()) {
+            SourceForBinaryQuery.Result2 result = SourceForBinaryQuery.findSourceRoots2(entry.getURL());
+            if (result.preferSources()) {
+                for (FileObject src : result.getRoots()) {
+                    for (URL bin : BinaryForSourceQuery.findBinaryRoots(src.getURL()).getRoots()) {
+                        if (!"file".equals(bin.getProtocol())) {
+                            continue;
+                        }
+                        File root;
+                        try {
+                            root = new File(bin.toURI());
+                        } catch (URISyntaxException x) {
+                            throw new IOException(x);
+                        }
+                        boolean found = new File(root, NB_COS).isFile();
+                        if (found) {
+                            toClean.add(root);
+                        }
+                        Logger.getLogger(CosChecker.class.getName()).log(Level.FINE, "found in {0}? {1}", new Object[] {root, found});
+                    }
+                }
+            }
+        }
+        Logger.getLogger(CosChecker.class.getName()).log(Level.FINE, "Cleaning NetBeans-generated class files from {0}", toClean);
+        if (toClean.isEmpty()) {
+            return;
+        }
         int res = JavaRunner.execute(JavaRunner.QUICK_CLEAN, Collections.singletonMap(
-                JavaRunner.PROP_EXECUTE_CLASSPATH, ClassPathSupport.createProxyClassPath(executePaths.toArray(new ClassPath[0])))).
+                JavaRunner.PROP_EXECUTE_CLASSPATH, exec)).
                 result();
         if (res != 0) {
             throw new IOException("Failed to clean NetBeans-generated classes");