diff --git a/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java b/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
index 12526e4de9d..9a4afa246bf 100644
--- a/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
+++ b/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskUpdatePackages.java
@@ -157,9 +157,21 @@ boolean lockVersionForNpm(ObjectNode packageJson) throws IOException {
                     // Already locked with a dependency reference, skip
                     continue;
                 }
+                // By the time the platform overrides are applied here, existing
+                // dependency versions are expected to be up-to-date already.
+                // So if there exists a dependency with a different version in
+                // package.json at this point, we assume it to be an explicit
+                // user opt-out. Skip such dependencies to avoid overriding them
+                // with a different version, both for "dependencies"
+                // and "devDependencies".
                 if (dependencies.has(dependency)
-                        || devDependencies.has(dependency)) {
-                    // Skip platform overrides for existing dependencies
+                        && !dependencies.get(dependency).asString()
+                                .equals(frontendVersion.getFullVersion())) {
+                    continue;
+                }
+                if (devDependencies.has(dependency)
+                        && !devDependencies.get(dependency).asString()
+                                .equals(frontendVersion.getFullVersion())) {
                     continue;
                 }
                 // Lock with a version number
diff --git a/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesNpmVersionLockingTest.java b/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesNpmVersionLockingTest.java
index 4c4d5d943d0..c1a0a38ece0 100644
--- a/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesNpmVersionLockingTest.java
+++ b/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/NodeUpdatePackagesNpmVersionLockingTest.java
@@ -137,6 +137,33 @@ void shouldNotUpdatesOverrides_whenHasUserModification()
                 packageJson.get(OVERRIDES).get(TEST_DEPENDENCY).stringValue());
     }
 
+    @Test
+    void shouldUpdatePlatformOverride_whenDependencyVersionBumped()
+            throws IOException {
+        TaskUpdatePackages packageUpdater = createPackageUpdater();
+
+        // Simulate existing platform override from a previous Flow version
+        ObjectNode packageJson = packageUpdater.getPackageJson();
+        ObjectNode overridesSection = JacksonUtils.createObjectNode();
+        packageJson.set(OVERRIDES, overridesSection);
+
+        ((ObjectNode) packageJson.get(DEPENDENCIES)).put(TEST_DEPENDENCY,
+                PLATFORM_PINNED_DEPENDENCY_VERSION);
+        overridesSection.put(TEST_DEPENDENCY, "0.0.1");
+
+        // vaadin.overrides tracks what Flow last wrote
+        ObjectNode vaadinSection = (ObjectNode) packageJson.get(VAADIN_DEP_KEY);
+        vaadinSection.set(OVERRIDES,
+                JacksonUtils.createObjectNode().put(TEST_DEPENDENCY, "0.0.1"));
+
+        packageUpdater.generateVersionsJson(packageJson);
+        packageUpdater.lockVersionForNpm(packageJson);
+
+        // Override is updated to the new platform version
+        assertEquals(PLATFORM_PINNED_DEPENDENCY_VERSION,
+                packageJson.get(OVERRIDES).get(TEST_DEPENDENCY).stringValue());
+    }
+
     @Test
     void shouldUpdatesOverrides_whenNoVaadinOverrides_changingVersion()
             throws IOException {