diff --git a/src/Microsoft.AspNetCore.Server.IISIntegration.Tools/WebConfigTransform.cs b/src/Microsoft.AspNetCore.Server.IISIntegration.Tools/WebConfigTransform.cs
index 563e2a00e..1db5cc8c8 100644
--- a/src/Microsoft.AspNetCore.Server.IISIntegration.Tools/WebConfigTransform.cs
+++ b/src/Microsoft.AspNetCore.Server.IISIntegration.Tools/WebConfigTransform.cs
@@ -60,7 +60,6 @@ private static void TransformAspNetCore(XElement aspNetCoreElement, string appNa
             // Forward slashes currently work neither in AspNetCoreModule nor in dotnet so they need to be
             // replaced with backwards slashes when the application is published on a non-Windows machine
             var appPath = Path.Combine(".", appName).Replace("/", "\\");
-            var logPath = Path.Combine(configureForAzure ? @"\\?\%home%\LogFiles" : @".\logs", "stdout").Replace("/", "\\");
             RemoveLauncherArgs(aspNetCoreElement);
 
             if (!isPortable)
@@ -85,7 +84,19 @@ private static void TransformAspNetCore(XElement aspNetCoreElement, string appNa
             }
 
             SetAttributeValueIfEmpty(aspNetCoreElement, "stdoutLogEnabled", "false");
-            SetAttributeValueIfEmpty(aspNetCoreElement, "stdoutLogFile", logPath);
+
+            var logPath = Path.Combine(configureForAzure ? @"\\?\%home%\LogFiles" : @".\logs", "stdout").Replace("/", "\\");
+            if (configureForAzure)
+            {
+                // When publishing for Azure we want to always overwrite path - the folder we set the path to
+                // will exist, the path is not easy to customize and stdoutLogPath should be only used for
+                // diagnostic purposes
+                aspNetCoreElement.SetAttributeValue("stdoutLogFile", logPath);
+            }
+            else
+            {
+                SetAttributeValueIfEmpty(aspNetCoreElement, "stdoutLogFile", logPath);
+            }
         }
 
         private static XElement GetOrCreateChild(XElement parent, string childName)
diff --git a/test/Microsoft.AspNetCore.Server.IISIntegration.Tools.Tests/WebConfigTransformFacts.cs b/test/Microsoft.AspNetCore.Server.IISIntegration.Tools.Tests/WebConfigTransformFacts.cs
index bc471ba76..d16314026 100644
--- a/test/Microsoft.AspNetCore.Server.IISIntegration.Tools.Tests/WebConfigTransformFacts.cs
+++ b/test/Microsoft.AspNetCore.Server.IISIntegration.Tools.Tests/WebConfigTransformFacts.cs
@@ -173,6 +173,17 @@ public void WebConfigTransform_correctly_configures_for_Azure()
                 aspNetCoreElement));
         }
 
+        [Fact]
+        public void WebConfigTransform_overwrites_stdoutLogPath_for_Azure()
+        {
+            var input = WebConfigTemplate;
+            var output = WebConfigTransform.Transform(input, "test.exe", configureForAzure: true, isPortable: false);
+
+            Assert.Equal(
+                @"\\?\%home%\LogFiles\stdout",
+                (string)output.Descendants("aspNetCore").Single().Attribute("stdoutLogFile"));
+        }
+
         [Fact]
         public void WebConfigTransform_configures_portable_apps_correctly()
         {