diff --git a/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/maven/dependency/ResolvedDependency.java b/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/maven/dependency/ResolvedDependency.java
index 0c068618940d8..e22e23a961671 100644
--- a/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/maven/dependency/ResolvedDependency.java
+++ b/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/maven/dependency/ResolvedDependency.java
@@ -5,6 +5,7 @@
 import io.quarkus.bootstrap.workspace.ArtifactSources;
 import io.quarkus.bootstrap.workspace.WorkspaceModule;
 import io.quarkus.paths.EmptyPathTree;
+import io.quarkus.paths.FilteredPathTree;
 import io.quarkus.paths.MultiRootPathTree;
 import io.quarkus.paths.PathCollection;
 import io.quarkus.paths.PathFilter;
@@ -36,7 +37,7 @@ default PathTree getContentTree(PathFilter pathFilter) {
         final WorkspaceModule module = getWorkspaceModule();
         final PathTree workspaceTree = module == null ? EmptyPathTree.getInstance() : module.getContentTree(getClassifier());
         if (!workspaceTree.isEmpty()) {
-            return workspaceTree;
+            return pathFilter == null ? workspaceTree : new FilteredPathTree(workspaceTree, pathFilter);
         }
         final PathCollection paths = getResolvedPaths();
         if (paths == null || paths.isEmpty()) {
diff --git a/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/paths/FilteredPathTree.java b/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/paths/FilteredPathTree.java
new file mode 100644
index 0000000000000..11e125a04fbf1
--- /dev/null
+++ b/independent-projects/bootstrap/app-model/src/main/java/io/quarkus/paths/FilteredPathTree.java
@@ -0,0 +1,99 @@
+package io.quarkus.paths;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Collection;
+import java.util.Objects;
+import java.util.function.Consumer;
+import java.util.function.Function;
+import java.util.jar.Manifest;
+
+public class FilteredPathTree implements PathTree {
+
+    private final PathTree original;
+    protected final PathFilter filter;
+
+    public FilteredPathTree(PathTree tree, PathFilter filter) {
+        this.original = Objects.requireNonNull(tree, "tree is null");
+        this.filter = Objects.requireNonNull(filter, "filter is null");
+    }
+
+    @Override
+    public Collection<Path> getRoots() {
+        return original.getRoots();
+    }
+
+    @Override
+    public Manifest getManifest() {
+        return original.getManifest();
+    }
+
+    @Override
+    public void walk(PathVisitor visitor) {
+        original.walk(visit -> {
+            if (visit != null && filter.isVisible(visit.getRelativePath("/"))) {
+                visitor.visitPath(visit);
+            }
+        });
+    }
+
+    @Override
+    public <T> T apply(String relativePath, Function<PathVisit, T> func) {
+        if (!PathFilter.isVisible(filter, relativePath)) {
+            return func.apply(null);
+        }
+        return original.apply(relativePath, func);
+    }
+
+    @Override
+    public void accept(String relativePath, Consumer<PathVisit> consumer) {
+        if (!PathFilter.isVisible(filter, relativePath)) {
+            consumer.accept(null);
+        } else {
+            original.accept(relativePath, consumer);
+        }
+    }
+
+    @Override
+    public boolean contains(String relativePath) {
+        return PathFilter.isVisible(filter, relativePath) && original.contains(relativePath);
+    }
+
+    @Override
+    public OpenPathTree open() {
+        return new OpenFilteredPathTree(original.open(), filter);
+    }
+
+    private static class OpenFilteredPathTree extends FilteredPathTree implements OpenPathTree {
+
+        private final OpenPathTree original;
+
+        private OpenFilteredPathTree(OpenPathTree original, PathFilter filter) {
+            super(original, filter);
+            this.original = original;
+        }
+
+        @Override
+        public PathTree getOriginalTree() {
+            return original.getOriginalTree();
+        }
+
+        @Override
+        public boolean isOpen() {
+            return original.isOpen();
+        }
+
+        @Override
+        public Path getPath(String relativePath) {
+            if (!PathFilter.isVisible(filter, relativePath)) {
+                return null;
+            }
+            return original.getPath(relativePath);
+        }
+
+        @Override
+        public void close() throws IOException {
+            original.close();
+        }
+    }
+}
diff --git a/independent-projects/bootstrap/app-model/src/test/java/io/quarkus/paths/FilteredPathTreeTest.java b/independent-projects/bootstrap/app-model/src/test/java/io/quarkus/paths/FilteredPathTreeTest.java
new file mode 100644
index 0000000000000..03a76ffea14f8
--- /dev/null
+++ b/independent-projects/bootstrap/app-model/src/test/java/io/quarkus/paths/FilteredPathTreeTest.java
@@ -0,0 +1,152 @@
+package io.quarkus.paths;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import io.quarkus.fs.util.ZipUtils;
+
+public class FilteredPathTreeTest {
+
+    @TempDir
+    static Path testDir;
+    static Path testJar;
+
+    private static void createFile(String path) throws Exception {
+        var file = testDir.resolve(path);
+        Files.createDirectories(file.getParent());
+        Files.createFile(file);
+    }
+
+    @BeforeAll
+    public static void beforeAll() throws Exception {
+        createFile("META-INF/jandex.idx");
+        createFile("org/toolbox/Axe.class");
+        createFile("org/toolbox/Hammer.class");
+        createFile("org/toolbox/Saw.class");
+        createFile("README.md");
+        testJar = testDir.resolve("test.jar");
+        ZipUtils.zip(testDir, testJar);
+    }
+
+    @Test
+    public void unfilteredTestDir() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testDir);
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "",
+                "META-INF",
+                "META-INF/jandex.idx",
+                "org",
+                "org/toolbox",
+                "org/toolbox/Axe.class",
+                "org/toolbox/Hammer.class",
+                "org/toolbox/Saw.class",
+                "README.md",
+                "test.jar");
+    }
+
+    @Test
+    public void unfilteredTestJar() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testJar);
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "",
+                "META-INF",
+                "META-INF/jandex.idx",
+                "org",
+                "org/toolbox",
+                "org/toolbox/Axe.class",
+                "org/toolbox/Hammer.class",
+                "org/toolbox/Saw.class",
+                "README.md",
+                "test.jar");
+    }
+
+    @Test
+    public void dirIncludeToolbox() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testDir, PathFilter.forIncludes(List.of("*/toolbox/**")));
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "org/toolbox/Axe.class",
+                "org/toolbox/Hammer.class",
+                "org/toolbox/Saw.class");
+    }
+
+    @Test
+    public void jarIncludeToolbox() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testJar, PathFilter.forIncludes(List.of("*/toolbox/**")));
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "org/toolbox/Axe.class",
+                "org/toolbox/Hammer.class",
+                "org/toolbox/Saw.class");
+    }
+
+    @Test
+    public void dirIncludeToolboxExcludeHammer() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testDir, new PathFilter(
+                List.of("*/toolbox/**"),
+                List.of("**/Hammer.class")));
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "org/toolbox/Axe.class",
+                "org/toolbox/Saw.class");
+    }
+
+    @Test
+    public void jarIncludeToolboxExcludeHammer() {
+        var pathTree = PathTree.ofDirectoryOrArchive(testJar, new PathFilter(
+                List.of("*/toolbox/**"),
+                List.of("**/Hammer.class")));
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "org/toolbox/Axe.class",
+                "org/toolbox/Saw.class");
+    }
+
+    @Test
+    public void filteredPathTree() throws Exception {
+        var originalFilter = new PathFilter(
+                List.of("*/toolbox/**"),
+                List.of("**/Hammer.class"));
+        var outerFilter = new PathFilter(
+                List.of("**/Axe.class"),
+                List.of("**/Saw.class"));
+
+        var pathTree = PathTree.ofDirectoryOrArchive(testDir, originalFilter);
+        pathTree = new FilteredPathTree(pathTree, outerFilter);
+        assertFilteredPathTree(pathTree);
+        try (var openTree = pathTree.open()) {
+            assertFilteredPathTree(openTree);
+        }
+
+        pathTree = PathTree.ofDirectoryOrArchive(testJar, originalFilter);
+        pathTree = new FilteredPathTree(pathTree, outerFilter);
+        assertFilteredPathTree(pathTree);
+        try (var openTree = pathTree.open()) {
+            assertFilteredPathTree(openTree);
+        }
+    }
+
+    private static void assertFilteredPathTree(PathTree pathTree) {
+        assertThat(getAllPaths(pathTree)).containsExactlyInAnyOrder(
+                "org/toolbox/Axe.class");
+
+        assertThat(pathTree.isEmpty()).isFalse();
+        assertThat(pathTree.contains("org/toolbox/Axe.class")).isTrue();
+        assertThat(pathTree.apply("org/toolbox/Axe.class", Objects::nonNull)).isTrue();
+        assertThat(pathTree.apply("org/toolbox/Saw.class", Objects::nonNull)).isFalse();
+        pathTree.accept("org/toolbox/Axe.class", visit -> assertThat(visit).isNotNull());
+        pathTree.accept("org/toolbox/Saw.class", visit -> assertThat(visit).isNull());
+    }
+
+    private static Set<String> getAllPaths(PathTree pathTree) {
+        final Set<String> paths = new HashSet<>();
+        pathTree.walk(visit -> paths.add(visit.getRelativePath("/")));
+        return paths;
+    }
+}