diff --git a/cli/ballerina-cli/src/main/java/io/ballerina/cli/cmd/CleanCommand.java b/cli/ballerina-cli/src/main/java/io/ballerina/cli/cmd/CleanCommand.java
index 6d28d9dbb972..6f8eff3fbe20 100644
--- a/cli/ballerina-cli/src/main/java/io/ballerina/cli/cmd/CleanCommand.java
+++ b/cli/ballerina-cli/src/main/java/io/ballerina/cli/cmd/CleanCommand.java
@@ -77,7 +77,20 @@ public void execute() {
             return;
         }
 
-        if (this.targetDir == null) {
+        if (this.targetDir != null) {
+            if (Files.notExists(this.targetDir)) {
+                CommandUtil.printError(this.outStream,
+                        "provided target directory '" + this.targetDir + "' does not exist.",
+                        null, false);
+            } else if (!Files.isDirectory(this.targetDir)) {
+                CommandUtil.printError(this.outStream,
+                        "provided target path '" + this.targetDir + "' is not a directory.",
+                        null, false);
+            } else {
+                ProjectUtils.deleteDirectory(this.targetDir);
+                this.outStream.println("Successfully deleted '" + this.targetDir + "'.");
+            }
+        } else {
             try {
                 Project project = BuildProject.load(this.projectPath);
                 this.targetDir = project.targetDir();
@@ -86,23 +99,13 @@ public void execute() {
                 CommandUtil.exitError(this.exitWhenFinish);
                 return;
             }
+            if (Files.exists(this.targetDir)) {
+                ProjectUtils.deleteDirectory(this.targetDir);
+                this.outStream.println("Successfully deleted '" + this.targetDir + "'.");
+            }
         }
 
-        // Delete the target directory
-        if (Files.notExists(this.targetDir)) {
-            CommandUtil.printError(this.outStream,
-                    "provided target directory '" + this.targetDir + "' does not exist.",
-                    null, false);
-        } else if (!Files.isDirectory(this.targetDir)) {
-            CommandUtil.printError(this.outStream,
-                    "provided target path '" + this.targetDir + "' is not a directory.",
-                    null, false);
-        } else {
-            ProjectUtils.deleteDirectory(this.targetDir);
-            this.outStream.println("Successfully deleted '" + this.targetDir + "'.");
-        }
-
-        //delete the generated directory
+        // delete the generated directory
         Path generatedDir;
         try {
             Project project = BuildProject.load(this.projectPath);