diff --git a/core/src/main/java/org/jboss/galleon/layout/ProvisioningLayout.java b/core/src/main/java/org/jboss/galleon/layout/ProvisioningLayout.java
index ca0aaff2..b2e9653e 100644
--- a/core/src/main/java/org/jboss/galleon/layout/ProvisioningLayout.java
+++ b/core/src/main/java/org/jboss/galleon/layout/ProvisioningLayout.java
@@ -1253,6 +1253,11 @@ private FeaturePackSpec.Builder getSpecRebuilder(FPID fpid, FeaturePackSpec fpSp
                 .initConfigs(fpSpec);
         rebuilder.addDefaultPackages(fpSpec.getDefaultPackageNames());
         rebuilder.setPatchFor(fpSpec.getPatchFor());
+        if (fpSpec.hasSystemPaths()) {
+            for (String systemPath : fpSpec.getSystemPaths()) {
+                rebuilder.addSystemPaths(systemPath);
+            }
+        }
         if(fpSpec.hasPlugins()) {
             for(Map.Entry<String, FeaturePackPlugin> entry : fpSpec.getPlugins().entrySet()) {
                 rebuilder.addPlugin(entry.getValue());
diff --git a/testsuite/src/test/java/org/jboss/galleon/userchanges/systemfiles/test/UserChangesAfterUpdatePlanWithDependencyTestCase.java b/testsuite/src/test/java/org/jboss/galleon/userchanges/systemfiles/test/UserChangesAfterUpdatePlanWithDependencyTestCase.java
new file mode 100644
index 00000000..0aa1cfff
--- /dev/null
+++ b/testsuite/src/test/java/org/jboss/galleon/userchanges/systemfiles/test/UserChangesAfterUpdatePlanWithDependencyTestCase.java
@@ -0,0 +1,138 @@
+/*
+ * Copyright 2016-2022 Red Hat, Inc. and/or its affiliates
+ * and other contributors as indicated by the @author tags.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.jboss.galleon.userchanges.systemfiles.test;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.jboss.galleon.ProvisioningDescriptionException;
+import org.jboss.galleon.ProvisioningException;
+import org.jboss.galleon.ProvisioningManager;
+import org.jboss.galleon.config.FeaturePackConfig;
+import org.jboss.galleon.config.ProvisioningConfig;
+import org.jboss.galleon.creator.FeaturePackCreator;
+import org.jboss.galleon.diff.FsDiff;
+import org.jboss.galleon.layout.ProvisioningPlan;
+import org.jboss.galleon.state.ProvisionedFeaturePack;
+import org.jboss.galleon.state.ProvisionedState;
+import org.jboss.galleon.test.util.fs.state.DirState;
+import org.jboss.galleon.universe.FeaturePackLocation;
+import org.jboss.galleon.universe.MvnUniverse;
+import org.jboss.galleon.userchanges.test.UserChangesTestBase;
+
+/**
+ *
+ * @author Alexey Loubyansky
+ */
+public class UserChangesAfterUpdatePlanWithDependencyTestCase extends UserChangesTestBase {
+
+    private FeaturePackLocation prod100;
+    private FeaturePackLocation prod101;
+    private FeaturePackLocation prod200;
+    private FeaturePackLocation prod201;
+
+    @Override
+    protected void createProducers(MvnUniverse universe) throws ProvisioningException {
+        universe.createProducer("prod1");
+        universe.createProducer("prod2");
+    }
+
+    @Override
+    protected void createFeaturePacks(FeaturePackCreator creator) throws ProvisioningException {
+
+        prod200 = newFpl("prod2", "1", "1.0.0.Final");
+        creator.newFeaturePack(prod200.getFPID())
+           .addSystemPaths("prod2/protected/")
+           .newPackage("p1", true)
+           .writeContent("prod2/protected/p1.txt", "prod2 p1");
+
+        prod201 = newFpl("prod2", "1", "1.0.1.Final");
+        creator.newFeaturePack(prod201.getFPID())
+           .addSystemPaths("prod2/protected/")
+           .newPackage("p1", true)
+           .writeContent("prod2/protected/p1.txt", "prod2 p2");
+
+        prod100 = newFpl("prod1", "1", "1.0.0.Final");
+        creator.newFeaturePack(prod100.getFPID())
+            .addSystemPaths("prod1/protected")
+            .addDependency(toMavenCoordsFpl(prod200))
+            .newPackage("p1", true)
+                .writeContent("prod1/protected/p1.txt", "prod1 p1")
+                .getFeaturePack();
+
+        prod101 = newFpl("prod1", "1", "1.0.1.Final");
+        creator.newFeaturePack(prod101.getFPID())
+            .addSystemPaths("prod1/protected")
+            .addDependency(toMavenCoordsFpl(prod201))
+            .newPackage("p1", true)
+                .writeContent("prod1/protected/p1.txt", "prod101 p1")
+                .getFeaturePack();
+
+    }
+
+    @Override
+    protected void testPm(ProvisioningManager pm) throws ProvisioningException {
+        pm.install(prod100);
+        writeContent("prod1/protected/new.txt", "user");
+        writeContent("prod1/protected/p1.txt", "user");
+        writeContent("prod2/protected/p1.txt", "user");
+
+        pm.apply(ProvisioningPlan.builder()
+                .install(prod101));
+    }
+
+
+    @Override
+    protected ProvisioningConfig provisionedConfig() throws ProvisioningDescriptionException {
+        return ProvisioningConfig.builder()
+                .addFeaturePackDep(FeaturePackConfig.builder(prod101)
+                        .build())
+                .build();
+    }
+
+    @Override
+    protected ProvisionedState provisionedState() throws ProvisioningException {
+        return ProvisionedState.builder()
+                .addFeaturePack(ProvisionedFeaturePack.builder(prod201.getFPID())
+                        .addPackage("p1")
+                        .build())
+                .addFeaturePack(ProvisionedFeaturePack.builder(prod101.getFPID())
+                        .addPackage("p1")
+                        .build())
+                .build();
+    }
+
+    @Override
+    protected DirState provisionedHomeDir() {
+        return newDirBuilder()
+                .addFile("prod1/protected/p1.txt", "prod101 p1")
+                .addFile("prod1/protected/p1.txt.glold", "user")
+                .addFile("prod2/protected/p1.txt", "prod2 p2")
+                .addFile("prod2/protected/p1.txt.glold", "user")
+                .addFile("prod1/protected/new.txt", "user")
+                .build();
+    }
+
+    @Override
+    protected List<String> expectedDiff() {
+        return Arrays.asList(
+                FsDiff.formatMessage(FsDiff.ADDED, "prod1/protected/new.txt", null),
+                FsDiff.formatMessage(FsDiff.FORCED, "prod1/protected/p1.txt", FsDiff.HAS_CHANGED_IN_THE_UPDATED_VERSION),
+                FsDiff.formatMessage(FsDiff.FORCED, "prod2/protected/p1.txt", FsDiff.HAS_CHANGED_IN_THE_UPDATED_VERSION)
+        );
+    }
+}