diff --git a/Tasks/AzureRmWebAppDeployment/azurermwebappdeployment.ts b/Tasks/AzureRmWebAppDeployment/azurermwebappdeployment.ts
index 460e7360ceb1..eda0db747ef0 100644
--- a/Tasks/AzureRmWebAppDeployment/azurermwebappdeployment.ts
+++ b/Tasks/AzureRmWebAppDeployment/azurermwebappdeployment.ts
@@ -27,7 +27,7 @@ async function main() {
         tl.setResourcePath(path.join( __dirname, 'task.json'));
         var taskParams: TaskParameters = TaskParametersUtility.getParameters();
         var azureEndpoint: AzureEndpoint = await new AzureRMEndpoint(taskParams.connectedServiceName).getEndpoint();
-
+        var virtualApplicationPath: string;
         console.log(tl.loc('GotconnectiondetailsforazureRMWebApp0', taskParams.WebAppName));
         if(!taskParams.DeployToSlotFlag) {
             taskParams.ResourceGroupName = await AzureResourceFilterUtility.getResourceGroupName(azureEndpoint, taskParams.WebAppName);
@@ -71,6 +71,7 @@ async function main() {
             if(taskParams.VirtualApplication) {
                 physicalPath = await appServiceUtility.getPhysicalPath(taskParams.VirtualApplication);
                 await kuduServiceUtility.createPathIfRequired(physicalPath);
+                virtualApplicationPath = physicalPath;
             }
 
             webPackage = await FileTransformsUtility.applyTransformations(webPackage, taskParams);
@@ -112,7 +113,7 @@ async function main() {
         }
 
         if(taskParams.ScriptType) {
-            await kuduServiceUtility.runPostDeploymentScript(taskParams);   
+            await kuduServiceUtility.runPostDeploymentScript(taskParams, virtualApplicationPath);   
         }
 
         await appServiceUtility.updateScmTypeAndConfigurationDetails();
diff --git a/Tasks/AzureRmWebAppDeployment/operations/KuduServiceUtility.ts b/Tasks/AzureRmWebAppDeployment/operations/KuduServiceUtility.ts
index 62ea06eeba72..f6a244986a09 100644
--- a/Tasks/AzureRmWebAppDeployment/operations/KuduServiceUtility.ts
+++ b/Tasks/AzureRmWebAppDeployment/operations/KuduServiceUtility.ts
@@ -34,23 +34,25 @@ export class KuduServiceUtility {
         }
     }
 
-    public async runPostDeploymentScript(taskParams: TaskParameters): Promise<void> {
+    public async runPostDeploymentScript(taskParams: TaskParameters, directoryPath?: string): Promise<void> {
         try {
+            directoryPath = (!!directoryPath) ? directoryPath : physicalRootPath.substring(1);
+
             if(taskParams.TakeAppOfflineFlag) {
-                await this._appOfflineKuduService(physicalRootPath, true);
+                await this._appOfflineKuduService(directoryPath, true);
             }
 
             var scriptFile = this._getPostDeploymentScript(taskParams.ScriptType, taskParams.InlineScript, taskParams.ScriptPath, taskParams.isLinuxApp);
             var uniqueID = this.getDeploymentID();
             var fileExtension : string = taskParams.isLinuxApp ? '.sh' : '.cmd';
             var mainCmdFilePath = path.join(__dirname, '..', 'postDeploymentScript', 'mainCmdFile' + fileExtension);
-            await this._appServiceKuduService.uploadFile(physicalRootPath, 'mainCmdFile_' + uniqueID + fileExtension, mainCmdFilePath);
-            await this._appServiceKuduService.uploadFile(physicalRootPath, 'kuduPostDeploymentScript_' + uniqueID + fileExtension, scriptFile.filePath);
+            await this._appServiceKuduService.uploadFile(directoryPath, 'mainCmdFile_' + uniqueID + fileExtension, mainCmdFilePath);
+            await this._appServiceKuduService.uploadFile(directoryPath, 'kuduPostDeploymentScript_' + uniqueID + fileExtension, scriptFile.filePath);
             console.log(tl.loc('ExecuteScriptOnKudu'));
-            await this.runCommand('site\\wwwroot',
+            await this.runCommand(directoryPath,
              'mainCmdFile_' + uniqueID + fileExtension + ' ' + uniqueID,
               30, 'script_result_' +  uniqueID + '.txt');
-            await this._printPostDeploymentLogs(physicalRootPath, uniqueID);
+            await this._printPostDeploymentLogs(directoryPath, uniqueID);
 
         }
         catch(error) {
@@ -58,14 +60,14 @@ export class KuduServiceUtility {
         }
         finally {
             try {
-                await this._appServiceKuduService.uploadFile(physicalRootPath, 'delete_log_file_' + uniqueID + fileExtension, path.join(__dirname, '..', 'postDeploymentScript', 'deleteLogFile' + fileExtension));
-                await this.runCommand('site\\wwwroot', 'delete_log_file_' + uniqueID + fileExtension + ' ' + uniqueID, 0, null);
+                await this._appServiceKuduService.uploadFile(directoryPath, 'delete_log_file_' + uniqueID + fileExtension, path.join(__dirname, '..', 'postDeploymentScript', 'deleteLogFile' + fileExtension));
+                await this.runCommand(directoryPath, 'delete_log_file_' + uniqueID + fileExtension + ' ' + uniqueID, 0, null);
             }
             catch(error) {
                 tl.debug('Unable to delete log files : ' + error);
             }
             if(taskParams.TakeAppOfflineFlag) {
-                await this._appOfflineKuduService(physicalRootPath, false);
+                await this._appOfflineKuduService(directoryPath, false);
             }
         }
     }
diff --git a/Tasks/AzureRmWebAppDeployment/task.json b/Tasks/AzureRmWebAppDeployment/task.json
index b7759180eec2..3037de424690 100644
--- a/Tasks/AzureRmWebAppDeployment/task.json
+++ b/Tasks/AzureRmWebAppDeployment/task.json
@@ -16,7 +16,7 @@
     "version": {
         "Major": 3,
         "Minor": 3,
-        "Patch": 38
+        "Patch": 39
     },
     "releaseNotes": "What's new in Version 3.0: <br/>&nbsp;&nbsp;Supports File Transformations (XDT) <br/>&nbsp;&nbsp;Supports Variable Substitutions(XML, JSON) <br/>Click [here](https://aka.ms/azurermwebdeployreadme) for more Information.",
     "minimumAgentVersion": "2.104.1",
diff --git a/Tasks/AzureRmWebAppDeployment/task.loc.json b/Tasks/AzureRmWebAppDeployment/task.loc.json
index 82cf7a3b5c5c..c976f5cd95db 100644
--- a/Tasks/AzureRmWebAppDeployment/task.loc.json
+++ b/Tasks/AzureRmWebAppDeployment/task.loc.json
@@ -16,7 +16,7 @@
   "version": {
     "Major": 3,
     "Minor": 3,
-    "Patch": 38
+    "Patch": 39
   },
   "releaseNotes": "ms-resource:loc.releaseNotes",
   "minimumAgentVersion": "2.104.1",