diff --git a/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/PathUtilities.cs b/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/PathUtilities.cs
index 5d276e3ae7..e685152da4 100644
--- a/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/PathUtilities.cs
+++ b/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/PathUtilities.cs
@@ -8,23 +8,31 @@ namespace Microsoft.AspNetCore.AzureAppServices.FunctionalTests
 {
     public class PathUtilities
     {
-        public static string[] GetStoreModules(string dotnetPath)
+        public static StoreModuleInfo[] GetStoreModules(string dotnetPath)
         {
             var dotnetHome = Path.GetDirectoryName(dotnetPath);
             return new DirectoryInfo(Path.Combine(dotnetHome, "store", "x64", "netcoreapp2.0"))
                 .GetDirectories()
-                .Select(d => d.Name)
+                .Select(d => new StoreModuleInfo
+                {
+                    Name = d.Name,
+                    Versions = d.GetDirectories().Select(GetName).ToArray()
+                })
                 .ToArray();
         }
 
-        public static string[] GetSharedRuntimeAssemblies(string dotnetPath)
+        public static string[] GetSharedRuntimeAssemblies(string dotnetPath, out string runtimeVersion)
         {
             var dotnetHome = Path.GetDirectoryName(dotnetPath);
-            return new DirectoryInfo(Path.Combine(dotnetHome, "shared", "Microsoft.NETCore.App"))
+            var runtimeDirectory = new DirectoryInfo(Path.Combine(dotnetHome, "shared", "Microsoft.NETCore.App"))
                 .GetDirectories()
-                .Single()
+                .Single();
+
+            runtimeVersion = runtimeDirectory.Name;
+
+            return runtimeDirectory
                 .GetFiles("*.dll")
-                .Select(f => f.Name)
+                .Select(GetName)
                 .ToArray();
         }
 
@@ -36,5 +44,13 @@ namespace Microsoft.AspNetCore.AzureAppServices.FunctionalTests
                 .Single()
                 .Name;
         }
+
+        private static string GetName(FileSystemInfo info) => info.Name;
+
+        public class StoreModuleInfo
+        {
+            public string Name { get; set; }
+            public string[] Versions { get; set; }
+        }
     }
 }
\ No newline at end of file
diff --git a/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/TemplateFunctionalTests.cs b/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/TemplateFunctionalTests.cs
index fd45e143ff..d3dfa3a0fe 100644
--- a/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/TemplateFunctionalTests.cs
+++ b/test/Microsoft.AspNetCore.AzureAppServices.FunctionalTests/TemplateFunctionalTests.cs
@@ -86,21 +86,37 @@ namespace Microsoft.AspNetCore.AzureAppServices.FunctionalTests
         private void ValidateRuntimeInfo(RuntimeInfo runtimeInfo, string dotnetPath)
         {
             var storeModules = PathUtilities.GetStoreModules(dotnetPath);
-
-            var runtimeModules = PathUtilities.GetSharedRuntimeAssemblies(dotnetPath);
+            var runtimeModules = PathUtilities.GetSharedRuntimeAssemblies(dotnetPath, out var runtimeVersion);
 
             foreach (var runtimeInfoModule in runtimeInfo.Modules)
             {
-                if (storeModules.Any(f => runtimeInfoModule.ModuleName.StartsWith(f, StringComparison.InvariantCultureIgnoreCase)))
+                var moduleName = Path.GetFileNameWithoutExtension(runtimeInfoModule.ModuleName);
+
+                // Check if module should come from the store, verify that one of the expected versions is loaded
+                var storeModule = storeModules.SingleOrDefault(f => moduleName.Equals(f.Name, StringComparison.InvariantCultureIgnoreCase));
+                if (storeModule != null)
                 {
-                    Assert.Contains("store\\x86\\netcoreapp2.0\\", runtimeInfoModule.FileName);
+                    var expectedVersion = false;
+                    foreach (var version in storeModule.Versions)
+                    {
+                        var expectedModulePath = $"store\\x86\\netcoreapp2.0\\{storeModule.Name}\\{version}";
+
+                        if (runtimeInfoModule.FileName.IndexOf(expectedModulePath, StringComparison.InvariantCultureIgnoreCase) != -1)
+                        {
+                            expectedVersion = true;
+                            break;
+                        }
+                    }
+
+                    Assert.True(expectedVersion, $"{runtimeInfoModule.FileName} doesn't match expected versions: {string.Join(",", storeModule.Versions)}");
                 }
 
+                // Verify that modules that we expect to come from runtime actually come from there
                 // Native modules would prefer to be loaded from windows folder, skip them
-                if (runtimeModules.Any(f => runtimeInfoModule.ModuleName.StartsWith(f, StringComparison.InvariantCultureIgnoreCase)) &&
+                if (runtimeModules.Any(rutimeModule => runtimeInfoModule.ModuleName.Equals(rutimeModule, StringComparison.InvariantCultureIgnoreCase)) &&
                     runtimeInfoModule.FileName.IndexOf("windows\\system32", StringComparison.InvariantCultureIgnoreCase) == -1)
                 {
-                    Assert.Contains("shared\\Microsoft.NETCore.App\\", runtimeInfoModule.FileName);
+                    Assert.Contains($"shared\\Microsoft.NETCore.App\\{runtimeVersion}", runtimeInfoModule.FileName);
                 }
             }
         }