diff --git a/flow-server/src/main/java/com/vaadin/flow/server/frontend/NodeUpdater.java b/flow-server/src/main/java/com/vaadin/flow/server/frontend/NodeUpdater.java
index 09519e4121c..2a684dcfebd 100644
--- a/flow-server/src/main/java/com/vaadin/flow/server/frontend/NodeUpdater.java
+++ b/flow-server/src/main/java/com/vaadin/flow/server/frontend/NodeUpdater.java
@@ -64,7 +64,7 @@ public abstract class NodeUpdater implements FallibleCommand {
     private static final String DEP_LICENSE_DEFAULT = "UNLICENSED";
     private static final String DEP_NAME_KEY = "name";
     private static final String DEP_NAME_DEFAULT = "no-name";
-    private static final String DEP_NAME_FLOW_DEPS = "@vaadin/flow-deps";
+    protected static final String DEP_NAME_FLOW_DEPS = "@vaadin/flow-deps";
     private static final String DEP_VERSION_KEY = "version";
     private static final String DEP_VERSION_DEFAULT = "1.0.0";
 
diff --git a/flow-server/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java b/flow-server/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
index ca80143a155..5f49860da8a 100644
--- a/flow-server/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
+++ b/flow-server/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
@@ -50,7 +50,7 @@
 public class TaskUpdatePackages extends NodeUpdater {
 
     static final String APP_PACKAGE_HASH = "vaadinAppPackageHash";
-    private static final String VALUE = "value";
+    private static final String VERSION = "version";
     private static final String SHRINK_WRAP = "@vaadin/vaadin-shrinkwrap";
     private boolean forceCleanUp;
 
@@ -207,8 +207,7 @@ private String getCurrentShrinkWrapVersion() throws IOException {
             return shrinkWrapVersion;
         }
 
-        File atVaadin = new File(nodeModulesFolder, "@vaadin");
-        File flowDeps = new File(atVaadin, "flow-deps");
+        File flowDeps = new File(nodeModulesFolder, DEP_NAME_FLOW_DEPS);
         shrinkWrapVersion = getShrinkWrapVersion(
                 getPackageJson(new File(flowDeps, Constants.PACKAGE_JSON)));
         if (shrinkWrapVersion != null) {
@@ -237,8 +236,8 @@ private String getPackageLockShrinkWrapVersion() throws IOException {
         }
 
         JsonObject shrinkWrap = dependencies.getObject(SHRINK_WRAP);
-        if (shrinkWrap.hasKey(VALUE)) {
-            return shrinkWrap.get(VALUE).asString();
+        if (shrinkWrap.hasKey(VERSION)) {
+            return shrinkWrap.get(VERSION).asString();
         }
         return null;
     }
diff --git a/flow-server/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesTest.java b/flow-server/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesTest.java
index a1e1af98c9c..4e80f9d2142 100644
--- a/flow-server/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesTest.java
+++ b/flow-server/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesTest.java
@@ -212,17 +212,64 @@ public void versions_doNotMatch_inPackageLock_cleanUp() throws IOException {
 
         assertVersionAndCleanUp();
     }
+    @Test
+    public void versionsDoNotMatch_inMainJson_cleanUp() throws IOException {
+        FrontendDependencies frontendDependencies = Mockito.mock(FrontendDependencies.class);
+
+        Map<String, String> packages = new HashMap<>();
+        packages.put("@polymer/iron-list", "3.0.2");
+        packages.put("@vaadin/vaadin-confirm-dialog", "1.1.4");
+        packages.put("@vaadin/vaadin-checkbox", "2.2.10");
+        packages.put("@polymer/iron-icon", "3.0.1");
+        packages.put("@vaadin/vaadin-time-picker", "2.0.2");
+        packages.put(SHRINKWRAP, "1.2.3");
+
+        Mockito.when(frontendDependencies.getPackages()).thenReturn(packages);
+
+        packageUpdater = new TaskUpdatePackages(null, frontendDependencies, baseDir,
+                generatedDir, false);
+
+        // Generate package json in a proper format first
+        packageCreator.execute();
+
+        makeNodeModulesAndPackageLock();
+
+        JsonObject packageJson = getPackageJson(mainPackageJson);
+        packageJson.put(SHRINKWRAP, "1.1.1");
+        Files.write(packageLock.toPath(),
+                Collections.singletonList(stringify(
+                        packageJson)));
+
+        packageUpdater.execute();
+
+        assertVersionAndCleanUp();
+    }
 
     @Test
     public void versionsMatch_noCleanUp() throws IOException {
+        FrontendDependencies frontendDependencies = Mockito.mock(FrontendDependencies.class);
+
+        Map<String, String> packages = new HashMap<>();
+        packages.put("@polymer/iron-list", "3.0.2");
+        packages.put("@vaadin/vaadin-confirm-dialog", "1.1.4");
+        packages.put("@vaadin/vaadin-checkbox", "2.2.10");
+        packages.put("@polymer/iron-icon", "3.0.1");
+        packages.put("@vaadin/vaadin-time-picker", "2.0.2");
+        packages.put(SHRINKWRAP, "1.1.1");
+
+        Mockito.when(frontendDependencies.getPackages()).thenReturn(packages);
+
+        packageUpdater = new TaskUpdatePackages(null, frontendDependencies, baseDir,
+                generatedDir, false);
+
         // Generate package json in a proper format first
         packageCreator.execute();
-        packageUpdater.execute();
 
         makeNodeModulesAndPackageLock();
 
-        // run it again with existing generated package.json and matched
-        // version
+        Files.write(packageLock.toPath(),
+                Collections.singletonList(stringify(makePackageLock("1.1.1"))));
+
         packageUpdater.execute();
 
         // nothing is removed