diff --git a/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt b/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt
new file mode 100644
index 0000000..da85fc2
--- /dev/null
+++ b/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt
@@ -0,0 +1,19 @@
+package app.revanced.cli.aligning
+
+import app.revanced.cli.command.MainCommand
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.utils.signing.align.ZipAligner
+import java.io.File
+
+object Aligning {
+    fun align(inputFile: File, outputFile: File) {
+        val cacheDirectory = File(MainCommand.args.sArgs?.pArgs?.cacheDirectory)
+        val alignedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
+
+        logger.info("Aligning ${inputFile.name}")
+        ZipAligner.align(inputFile, alignedOutput)
+
+        logger.info("Copying ${alignedOutput.name} to ${outputFile.name}")
+        alignedOutput.copyTo(outputFile, true)
+        }
+    }
diff --git a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
index 0616a4a..d0b057b 100644
--- a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
@@ -1,5 +1,6 @@
 package app.revanced.cli.command
 
+import app.revanced.cli.aligning.Aligning
 import app.revanced.cli.logging.impl.DefaultCliLogger
 import app.revanced.cli.patcher.Patcher
 import app.revanced.cli.patcher.logging.impl.PatcherLogger
@@ -162,8 +163,7 @@ internal object MainCommand : Runnable {
         val adb: Adb? = _args.deploy?.let {
             Adb(outputFile, patcher.data.packageMetadata.packageName, _args.deploy!!, !args.mount)
         }
-        val patchedFile = if (args.mount) outputFile
-        else File(args.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
+        val patchedFile = File(args.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
 
         Patcher.start(patcher, patchedFile)
 
@@ -180,6 +180,9 @@ internal object MainCommand : Runnable {
                 )
             )
         }
+        else {
+            Aligning.align(patchedFile, outputFile)
+        }
 
         if (args.clean) File(args.cacheDirectory).deleteRecursively()
 
diff --git a/src/main/kotlin/app/revanced/cli/signing/Signing.kt b/src/main/kotlin/app/revanced/cli/signing/Signing.kt
index 677316f..2d44199 100644
--- a/src/main/kotlin/app/revanced/cli/signing/Signing.kt
+++ b/src/main/kotlin/app/revanced/cli/signing/Signing.kt
@@ -7,14 +7,14 @@ import app.revanced.utils.signing.align.ZipAligner
 import java.io.File
 
 object Signing {
-    fun start(inputFile: File, outputFile: File, signingOptions: SigningOptions) {
+    fun start(patchedFile: File, outputFile: File, signingOptions: SigningOptions) {
         val cacheDirectory = File(args.sArgs?.pArgs?.cacheDirectory)
-        val alignedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
         val signedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_signed.apk")
+        val alignedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
+
+        // align the patchedFile and write to alignedFile
+        ZipAligner.align(patchedFile, alignedOutput)
 
-        // align the inputFile and write to alignedOutput
-        logger.info("Aligning ${inputFile.name}")
-        ZipAligner.align(inputFile, alignedOutput)
         // sign the alignedOutput and write to signedOutput
         // the reason is, in case the signer fails
         // it does not damage the output file