diff --git a/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFiles.java b/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFiles.java
index 8e8a2fa857a..71b0b54b203 100644
--- a/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFiles.java
+++ b/flow-build-tools/src/main/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFiles.java
@@ -36,9 +36,17 @@
 /**
  * Copies all frontend resources from JAR files into a given folder.
  * <p>
- * The task considers "frontend resources" all files placed in
- * {@literal META-INF/frontend}, {@literal META-INF/resources/frontend} and
- * {@literal META-INF/resources/[**]/themes} folders.
+ * "Frontend resources" are bundle sources for {@code @JsModule} /
+ * {@code @CssImport} annotations. The recommended location for them in addon
+ * JARs is {@literal META-INF/frontend}. The legacy location
+ * {@literal META-INF/resources/frontend} is still scanned for backwards
+ * compatibility but is deprecated; a per-jar warning is emitted when it is
+ * used. Theme files under {@literal META-INF/resources/[**]/themes} are also
+ * copied.
+ * <p>
+ * Public runtime resources for {@code @StyleSheet} / {@code @JavaScript} should
+ * be placed under {@literal META-INF/resources/} and are served directly by the
+ * servlet container — they are not handled by this task.
  * <p>
  * For internal use only. May be renamed or removed in a future release.
  *
@@ -49,6 +57,7 @@ public class TaskCopyFrontendFiles
     private static final String WILDCARD_INCLUSION_APP_THEME_JAR = "**/themes/**/*";
     private final Options options;
     private final Set<File> resourceLocations;
+    private final Set<File> warnedLegacyLocations = new HashSet<>();
 
     /**
      * Scans the jar files given defined by {@code resourcesToScan}.
@@ -85,10 +94,13 @@ public void execute() {
                         .addAll(TaskCopyLocalFrontendFiles.copyLocalResources(
                                 new File(location, RESOURCES_FRONTEND_DEFAULT),
                                 targetDirectory));
+                File legacyDir = new File(location,
+                        COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT);
+                if (legacyDir.isDirectory()) {
+                    warnAboutDeprecatedFrontendLayout(location);
+                }
                 handledFiles.addAll(TaskCopyLocalFrontendFiles
-                        .copyLocalResources(new File(location,
-                                COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT),
-                                targetDirectory));
+                        .copyLocalResources(legacyDir, targetDirectory));
                 // copies from resources, but excludes already copied from
                 // resources/frontend
                 handledFiles
@@ -100,6 +112,10 @@ public void execute() {
                         .copyIncludedFilesFromJarTrimmingBasePath(location,
                                 RESOURCES_FRONTEND_DEFAULT, targetDirectory,
                                 "**/*"));
+                if (jarContentsManager.containsPath(location,
+                        COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT + "/")) {
+                    warnAboutDeprecatedFrontendLayout(location);
+                }
                 handledFiles.addAll(jarContentsManager
                         .copyIncludedFilesFromJarTrimmingBasePath(location,
                                 COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT,
@@ -136,4 +152,16 @@ private Logger log() {
         return LoggerFactory.getLogger(this.getClass());
     }
 
+    private void warnAboutDeprecatedFrontendLayout(File location) {
+        if (warnedLegacyLocations.add(location)) {
+            log().warn("Addon '{}' contains frontend sources under {}/. "
+                    + "This location is deprecated; migrate them to {}/ "
+                    + "(bundle sources for @JsModule/@CssImport) or to "
+                    + "META-INF/resources/ (runtime resources for "
+                    + "@StyleSheet/@JavaScript).", location.getName(),
+                    COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT,
+                    RESOURCES_FRONTEND_DEFAULT);
+        }
+    }
+
 }
diff --git a/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFilesTest.java b/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFilesTest.java
index 54ccec7336b..a47428efcee 100644
--- a/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFilesTest.java
+++ b/flow-build-tools/src/test/java/com/vaadin/flow/server/frontend/TaskCopyFrontendFilesTest.java
@@ -26,12 +26,18 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.mockito.MockedStatic;
+import org.mockito.Mockito;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import tools.jackson.databind.JsonNode;
 
 import com.vaadin.flow.testutil.TestUtils;
 import com.vaadin.tests.util.MockOptions;
 
+import static com.vaadin.flow.server.Constants.COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT;
 import static com.vaadin.flow.server.Constants.PACKAGE_JSON;
+import static com.vaadin.flow.server.Constants.RESOURCES_FRONTEND_DEFAULT;
 import static com.vaadin.flow.server.Constants.TARGET;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -94,6 +100,58 @@ void should_createPackageJson() throws IOException {
         assertFalse(deps.has(NodeUpdater.DEP_NAME_FLOW_JARS));
     }
 
+    @Test
+    void should_warnOnceAboutLegacyLayout_whenJarUsesLegacyLocation() {
+        File legacyJar = TestUtils
+                .getTestJar("jar-with-frontend-resources.jar");
+        TaskCopyFrontendFiles task = taskFor(legacyJar);
+
+        Logger logger = Mockito.spy(Logger.class);
+        try (MockedStatic<LoggerFactory> loggerFactoryMocked = Mockito
+                .mockStatic(LoggerFactory.class)) {
+            loggerFactoryMocked
+                    .when(() -> LoggerFactory.getLogger(task.getClass()))
+                    .thenReturn(logger);
+
+            // Two runs of the same task instance should still warn only once
+            task.execute();
+            task.execute();
+
+            Mockito.verify(logger, Mockito.times(1)).warn(
+                    Mockito.contains("deprecated"),
+                    Mockito.eq(legacyJar.getName()),
+                    Mockito.eq(COMPATIBILITY_RESOURCES_FRONTEND_DEFAULT),
+                    Mockito.eq(RESOURCES_FRONTEND_DEFAULT));
+        }
+    }
+
+    @Test
+    void should_notWarnAboutLegacyLayout_whenJarUsesModernLocation() {
+        TaskCopyFrontendFiles task = taskFor(
+                TestUtils.getTestJar("jar-with-modern-frontend.jar"));
+
+        Logger logger = Mockito.spy(Logger.class);
+        try (MockedStatic<LoggerFactory> loggerFactoryMocked = Mockito
+                .mockStatic(LoggerFactory.class)) {
+            loggerFactoryMocked
+                    .when(() -> LoggerFactory.getLogger(task.getClass()))
+                    .thenReturn(logger);
+
+            task.execute();
+
+            Mockito.verify(logger, Mockito.never()).warn(
+                    Mockito.contains("deprecated"), Mockito.<Object> any(),
+                    Mockito.<Object> any(), Mockito.<Object> any());
+        }
+    }
+
+    private TaskCopyFrontendFiles taskFor(File... locations) {
+        Options options = new MockOptions(null);
+        options.withJarFrontendResourcesFolder(frontendDepsFolder)
+                .copyResources(jars(locations));
+        return new TaskCopyFrontendFiles(options);
+    }
+
     private void should_collectJsAndCssFilesFromJars(String jarFile,
             String fsDir) throws IOException {