diff --git a/maven-plugin/src/main/java/io/github/project/classport/plugin/EmbeddingMojo.java b/maven-plugin/src/main/java/io/github/project/classport/plugin/EmbeddingMojo.java
index 970bc8e..467601c 100644
--- a/maven-plugin/src/main/java/io/github/project/classport/plugin/EmbeddingMojo.java
+++ b/maven-plugin/src/main/java/io/github/project/classport/plugin/EmbeddingMojo.java
@@ -34,7 +34,7 @@
 import io.github.project.classport.commons.ClassportInfo;
 import io.github.project.classport.commons.Utility;
 
-@Mojo(name = "embed", defaultPhase = LifecyclePhase.COMPILE, requiresDependencyResolution = ResolutionScope.COMPILE_PLUS_RUNTIME)
+@Mojo(name = "embed", defaultPhase = LifecyclePhase.PROCESS_CLASSES, requiresDependencyResolution = ResolutionScope.COMPILE_PLUS_RUNTIME)
 public class EmbeddingMojo
         extends AbstractMojo {
     /**
@@ -121,16 +121,6 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
         });
     }
 
-    /**
-     * Root directory (shared by all modules) where embedded artefacts are written
-     * in Maven-repository layout.
-     * We keep the name "classport-files" to maintain backward compatibility with the previous version of the plugin.
-     */
-    private File getAggregatedRepoRoot() {
-        File topLevelBaseDir = session.getTopLevelProject().getBasedir();
-        return new File(topLevelBaseDir, "classport-files");
-    }
-
     /**
      * Destination path (jar) inside the aggregated repository for the given
      * artifact.
@@ -165,6 +155,7 @@ private void embedArtifactIntoRepo(Artifact artifact, File repoRoot)
         destJar.getParentFile().mkdirs();
 
         Files.copy(artifactFile.toPath(), destJar.toPath(), StandardCopyOption.REPLACE_EXISTING);
+        getLog().info(String.format("Copied artifact %s to %s", artifactFile.getAbsolutePath(), destJar.getAbsolutePath()));
 
         ClassportInfo meta = getMetadata(artifact);
         File tempJar = new File(destJar.getParent(), destJar.getName() + ".tmp");
@@ -174,17 +165,17 @@ private void embedArtifactIntoRepo(Artifact artifact, File repoRoot)
         Files.delete(destJar.toPath());
         Files.move(tempJar.toPath(), destJar.toPath(), StandardCopyOption.REPLACE_EXISTING);
 
-        getLog().info("Embedded artifact into aggregated repo: " + destJar.getAbsolutePath());
+        getLog().info("Embedded metadata into: " + destJar.getAbsolutePath());
+        
+        // This makes Maven packaging plugins use the embedded JAR
+        artifact.setFile(destJar);
+        getLog().debug("Updated artifact reference: " + artifact.getId() + " -> " + destJar.getAbsolutePath());
     }
 
     @Override
     public void execute() throws MojoExecutionException, MojoFailureException {
         Set<Artifact> dependencyArtifacts = project.getArtifacts();
 
-        // Shared repository for all modules
-        File aggregatedRepoRoot = getAggregatedRepoRoot();
-        aggregatedRepoRoot.mkdirs();
-
         getLog().info("Embedding metadata into compiled classes for module: " + project.getArtifactId());
         try {
             embedDirectory(project.getArtifact(), classesDirectory);
@@ -197,11 +188,12 @@ public void execute() throws MojoExecutionException, MojoFailureException {
         getLog().info("Processing dependencies");
         for (Artifact artifact : dependencyArtifacts) {
             try {
-                embedArtifactIntoRepo(artifact, aggregatedRepoRoot);
+                File classportFilesDir = new File(project.getBuild().getDirectory(), "classport-files");
+                classportFilesDir.mkdirs();
+                embedArtifactIntoRepo(artifact, classportFilesDir);
             } catch (IOException e) {
                 getLog().error("Failed to embed metadata for " + artifact + ": " + e);
             }
-
         }
     }
 
@@ -215,7 +207,7 @@ private ClassportInfo getMetadata(Artifact artifact) throws IOException, MojoExe
                 .collect(Collectors.toList()).contains(aId);
 
         return new ClassportHelper().getInstance(
-                getArtifactLongId(project.getArtifact()), // TODO: Make into a constant
+                getArtifactLongId(project.getArtifact()),
                 isDirectDependency,
                 aId,
                 artifact.getArtifactId(),
diff --git a/maven-plugin/src/test/java/io/github/project/classport/plugin/it/EmbeddingMojoIT.java b/maven-plugin/src/test/java/io/github/project/classport/plugin/it/EmbeddingMojoIT.java
index 99d4ffa..02738e3 100644
--- a/maven-plugin/src/test/java/io/github/project/classport/plugin/it/EmbeddingMojoIT.java
+++ b/maven-plugin/src/test/java/io/github/project/classport/plugin/it/EmbeddingMojoIT.java
@@ -9,7 +9,6 @@
 import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.junit.jupiter.api.Disabled;
 
 import com.soebes.itf.jupiter.extension.MavenGoal;
 import com.soebes.itf.jupiter.extension.MavenJupiterExtension;
@@ -20,7 +19,6 @@
 import io.github.project.classport.analyser.CorrectnessAnalyser;
 import io.github.project.classport.commons.ClassportInfo;
 
-@Disabled("Skipping this test until we find a way to embed using a single command")
 @MavenJupiterExtension
 public class EmbeddingMojoIT {
     @MavenGoal("package")
@@ -44,6 +42,13 @@ void embed_dependency_simple_app(MavenExecutionResult result) {
         Set<String> expectedIds = Set.of("org.apache.commons:commons-lang3:jar:3.17.0", "org.example:hello:jar:0.1.0");
         Set<String> actualIds = sbom.values().stream().map(ClassportInfo::id).collect(Collectors.toSet());
         assertEquals(expectedIds, actualIds);
+        // Make sure that dependency in m2 repository is not embedded
+        Path m2Repository = Paths.get("target/maven-it/io/github/project/classport/plugin/it/EmbeddingMojoIT/embed_dependency_simple_app/.m2/repository");
+        try (JarFile m2RepositoryJar = new JarFile(m2Repository.resolve("org/apache/commons/commons-lang3/3.17.0/commons-lang3-3.17.0.jar").toFile())) {
+            HashMap<String, ClassportInfo> m2RepositorySbom = CorrectnessAnalyser.getSBOM(m2RepositoryJar);
+            assertEquals(0, m2RepositorySbom.size());
+        } catch (IOException e) {
+            throw new RuntimeException("Failed to open m2 repository jar", e);
+        }
     }
-
 }