diff --git a/src/WebJobs.Script/Description/PowerShell/PowerShellFunctionInvoker.cs b/src/WebJobs.Script/Description/PowerShell/PowerShellFunctionInvoker.cs
index ccc000af09..d3ba3bfa32 100644
--- a/src/WebJobs.Script/Description/PowerShell/PowerShellFunctionInvoker.cs
+++ b/src/WebJobs.Script/Description/PowerShell/PowerShellFunctionInvoker.cs
@@ -87,7 +87,9 @@ private async Task<PSDataCollection<ErrorRecord>> InvokePowerShellScript(Diction
                         System.Management.Automation.PowerShell.Create())
                 {
                     powerShellInstance.Runspace = runspace;
-                    _moduleFiles = GetModuleFilePaths(_host.ScriptConfig.RootScriptPath, _functionName);
+                    _moduleFiles = FindDuplicateModules(GetModuleFilePaths(_host.ScriptConfig.RootScriptPath, _functionName), _host.ScriptConfig.RootScriptPath, _functionName);
+                    // Remove duplicates from _moduleFiles and only keep the ones closest to the Function in moduleDirectory
+
                     if (_moduleFiles.Any())
                     {
                         powerShellInstance.AddCommand("Import-Module").AddArgument(_moduleFiles);
@@ -261,18 +263,58 @@ internal static List<string> GetModuleFilePaths(string rootScriptPath, string fu
         {
             List<string> modulePaths = new List<string>();
             string functionFolder = Path.Combine(rootScriptPath, functionName);
+            string rootModuleDirectory = Path.Combine(rootScriptPath, PowerShellConstants.ModulesFolderName);
             string moduleDirectory = Path.Combine(functionFolder, PowerShellConstants.ModulesFolderName);
-            if (Directory.Exists(moduleDirectory))
+            modulePaths.AddRange(AddToModulePaths(rootModuleDirectory, moduleDirectory));
+            return modulePaths;
+        }
+
+        internal static List<string> AddToModulePaths(params string[] directories)
+        {
+            List<string> paths = new List<string>();
+            foreach (string directory in directories)
             {
-                modulePaths.AddRange(Directory.GetFiles(moduleDirectory,
-                    PowerShellConstants.ModulesManifestFileExtensionPattern));
-                modulePaths.AddRange(Directory.GetFiles(moduleDirectory,
-                    PowerShellConstants.ModulesBinaryFileExtensionPattern));
-                modulePaths.AddRange(Directory.GetFiles(moduleDirectory,
-                    PowerShellConstants.ModulesScriptFileExtensionPattern));
+                if (Directory.Exists(directory))
+                {
+                    paths.AddRange(Directory.GetFiles(directory,
+                        PowerShellConstants.ModulesManifestFileExtensionPattern,
+                        SearchOption.AllDirectories));
+                    paths.AddRange(Directory.GetFiles(directory,
+                        PowerShellConstants.ModulesBinaryFileExtensionPattern,
+                        SearchOption.AllDirectories));
+                    paths.AddRange(Directory.GetFiles(directory,
+                        PowerShellConstants.ModulesScriptFileExtensionPattern,
+                        SearchOption.AllDirectories));
+                }
             }
+            return paths;
+        }
 
-            return modulePaths;
+        internal static List<string> FindDuplicateModules(List<string> foundModules, string rootScriptPath, string functionName)
+        {
+            List<string> moduleFileNames = new List<string>();
+            string functionFolder = Path.Combine(rootScriptPath, functionName);
+            string rootModuleDirectory = Path.Combine(rootScriptPath, PowerShellConstants.ModulesFolderName);
+            string moduleDirectory = Path.Combine(functionFolder, PowerShellConstants.ModulesFolderName);
+
+            foreach (string entry in foundModules)
+            {
+                moduleFileNames.Add(Path.GetFileName(entry));
+            }
+
+            List<string> distinctModuleFiles = moduleFileNames.Distinct().ToList();
+
+            foreach (string distinctModuleFile in distinctModuleFiles)
+            {
+                string potentialModule = Path.Combine(moduleDirectory, distinctModuleFile);
+                string result = foundModules.SingleOrDefault(s => s == potentialModule);
+                if (result != null)
+                {
+                    foundModules.Remove(Path.Combine(rootModuleDirectory, distinctModuleFile));
+                }
+            }
+            return foundModules;
         }
+
     }
 }
diff --git a/test/WebJobs.Script.Tests/Description/PowerShell/PowerShellInvokerTests.cs b/test/WebJobs.Script.Tests/Description/PowerShell/PowerShellInvokerTests.cs
index 7af142c45c..2231333b71 100644
--- a/test/WebJobs.Script.Tests/Description/PowerShell/PowerShellInvokerTests.cs
+++ b/test/WebJobs.Script.Tests/Description/PowerShell/PowerShellInvokerTests.cs
@@ -37,6 +37,17 @@ public void GetModuleFilePaths()
             }
         }
 
+        [Fact]
+        public void FindDuplicateModules()
+        {
+            List<string> actualModules = PowerShellFunctionInvoker.FindDuplicateModules(PowerShellFunctionInvoker.GetModuleFilePaths(_fixture.TestRootScriptPath, _fixture.TestFunctionName), _fixture.TestRootScriptPath, _fixture.TestFunctionName);
+            Assert.Equal(_fixture.ExpectedNumberOfImportedModules, actualModules.Count);
+            foreach (var actualModule in actualModules)
+            {
+                Assert.True(_fixture.TestModulesPath.Contains(actualModule));
+            }
+        }
+
         [Fact]
         public void GetRelativePath()
         {
@@ -90,6 +101,9 @@ public Fixture()
                 TestRootScriptPath = Path.Combine(TestHelpers.FunctionsTestDirectory, "Functions");
                 TestFunctionRoot = Path.Combine(TestRootScriptPath, TestFunctionName);
                 TestModulesRoot = Path.Combine(TestFunctionRoot, "modules");
+                // The number of imported modules is expected to be 6, as the "manifest-module.psd1" in RootTestModules
+                // should be ignored when importing. So the 7 available modules should end up being 6.
+                ExpectedNumberOfImportedModules = 6;
 
                 TestScriptPath = CreateScriptFile(TestFunctionRoot);
 
@@ -100,7 +114,15 @@ public Fixture()
                     "manifest-module.psd1"
                 };
 
-                TestModulesPath = CreateModuleFiles(TestModulesRoot, TestModules);
+                RootTestModules = new string[]
+                {
+                    "root-script-module.psm1",
+                    "root-binary-module.dll",
+                    "root-manifest-module.psd1",
+                    "manifest-module.psd1"
+                };
+
+                TestModulesPath = CreateModuleFiles(TestModulesRoot, RootTestModules, TestModules);
             }
 
             public string TestFunctionRoot { get; private set; }
@@ -115,9 +137,12 @@ public Fixture()
 
             public string[] TestModules { get; private set; }
 
+            public string[] RootTestModules { get; private set; }
+
             public string TestModulesRoot { get; private set; }
 
             public List<string> TestModulesPath { get; set; }
+            public int ExpectedNumberOfImportedModules { get; set; }
 
             public void Dispose()
             {
@@ -154,13 +179,20 @@ public string CreateScriptFile(string scriptRoot)
                 return path;
             }
 
-            public List<string> CreateModuleFiles(string moduleRoot, string[] modules)
+            public List<string> CreateModuleFiles(string moduleRoot, string[] rootModules, string[] modules)
             {
                 if (!Directory.Exists(moduleRoot))
                 {
                     Directory.CreateDirectory(moduleRoot);
                 }
 
+                string moduleDirinRoot = TestRootScriptPath + "\\modules";
+
+                if (!Directory.Exists(moduleDirinRoot))
+                {
+                    Directory.CreateDirectory(moduleDirinRoot);
+                }
+                
                 List<string> modulesPath = new List<string>();
                 foreach (var module in modules)
                 {
@@ -177,6 +209,21 @@ public List<string> CreateModuleFiles(string moduleRoot, string[] modules)
                     modulesPath.Add(path);
                 }
 
+                foreach (var rootModule in rootModules)
+                {
+                    string path = Path.Combine(moduleDirinRoot, rootModule);
+                    if (!File.Exists(path))
+                    {
+                        // Create a file to write to.
+                        using (StreamWriter sw = File.CreateText(path))
+                        {
+                            sw.WriteLine(string.Format("This is a {0} file.", rootModule));
+                        }
+                    }
+
+                    modulesPath.Add(path);
+                }
+
                 return modulesPath;
             }
         }