diff --git a/brut.apktool/apktool-lib/src/main/java/brut/androlib/res/AndrolibResources.java b/brut.apktool/apktool-lib/src/main/java/brut/androlib/res/AndrolibResources.java
index 5a695e66..a896bd39 100644
--- a/brut.apktool/apktool-lib/src/main/java/brut/androlib/res/AndrolibResources.java
+++ b/brut.apktool/apktool-lib/src/main/java/brut/androlib/res/AndrolibResources.java
@@ -563,10 +563,17 @@ final public class AndrolibResources {
             cmd.add("-x");
         }
 
-        if (apkOptions.doNotCompress != null) {
+        if (apkOptions.doNotCompress != null && !customAapt) {
+            // Use custom -e option to avoid limits on commandline length.
+            // Can only be used when custom aapt binary is not used.
             String extensionsFilePath = createDoNotCompressExtensionsFile(apkOptions).getAbsolutePath();
             cmd.add("-e");
             cmd.add(extensionsFilePath);
+        } else if (apkOptions.doNotCompress != null) {
+            for (String file : apkOptions.doNotCompress) {
+                cmd.add("-0");
+                cmd.add(file);
+            }
         }
 
         if (!apkOptions.resourcesAreCompressed) {