diff --git a/java/base.go b/java/base.go
index c828503d4..25cc68fb0 100644
--- a/java/base.go
+++ b/java/base.go
@@ -1217,12 +1217,6 @@ func (j *Module) compile(ctx android.ModuleContext, aaptSrcJar android.Path) {
 				return
 			}
 
-			// Initialize the hiddenapi structure.
-			j.initHiddenAPI(ctx, dexOutputFile, j.implementationJarFile, j.dexProperties.Uncompress_dex)
-
-			// Encode hidden API flags in dex file.
-			dexOutputFile = j.hiddenAPIEncodeDex(ctx, dexOutputFile)
-
 			// merge dex jar with resources if necessary
 			if j.resourceJar != nil {
 				jars := android.Paths{dexOutputFile, j.resourceJar}
@@ -1238,6 +1232,12 @@ func (j *Module) compile(ctx android.ModuleContext, aaptSrcJar android.Path) {
 				}
 			}
 
+			// Initialize the hiddenapi structure.
+			j.initHiddenAPI(ctx, dexOutputFile, j.implementationJarFile, j.dexProperties.Uncompress_dex)
+
+			// Encode hidden API flags in dex file, if needed.
+			dexOutputFile = j.hiddenAPIEncodeDex(ctx, dexOutputFile)
+
 			j.dexJarFile = dexOutputFile
 
 			// Dexpreopting
diff --git a/java/hiddenapi.go b/java/hiddenapi.go
index 1e838247b..c9e3c29a3 100644
--- a/java/hiddenapi.go
+++ b/java/hiddenapi.go
@@ -235,7 +235,7 @@ var hiddenAPIEncodeDexRule = pctx.AndroidStaticRule("hiddenAPIEncodeDex", bluepr
 		  echo "--output-dex=$tmpDir/dex-output/$$(basename $${INPUT_DEX})";
 		done | xargs ${config.HiddenAPI} encode --api-flags=$flagsCsv $hiddenapiFlags &&
 		${config.SoongZipCmd} $soongZipFlags -o $tmpDir/dex.jar -C $tmpDir/dex-output -f "$tmpDir/dex-output/classes*.dex" &&
-		${config.MergeZipsCmd} -D -zipToNotStrip $tmpDir/dex.jar -stripFile "classes*.dex" -stripFile "**/*.uau" $out $tmpDir/dex.jar $in`,
+		${config.MergeZipsCmd} -j -D -zipToNotStrip $tmpDir/dex.jar -stripFile "classes*.dex" -stripFile "**/*.uau" $out $tmpDir/dex.jar $in`,
 	CommandDeps: []string{
 		"${config.HiddenAPI}",
 		"${config.SoongZipCmd}",