diff --git a/GitTfs/Commands/Clone.cs b/GitTfs/Commands/Clone.cs
index 43d69ae2..2d614cb8 100644
--- a/GitTfs/Commands/Clone.cs
+++ b/GitTfs/Commands/Clone.cs
@@ -118,6 +118,8 @@ namespace Sep.Git.Tfs.Commands
                 if (tfsRepositoryPath == GitTfsConstants.TfsRoot)
                     fetch.IgnoreBranches = true;
 
+                globals.Repository.SetConfig(GitTfsConstants.IgnoreBranches, fetch.IgnoreBranches.ToString());
+
                 if (retVal == 0)
                 {
                     fetch.Run(withBranches);
diff --git a/GitTfs/Commands/Init.cs b/GitTfs/Commands/Init.cs
index de48ebe0..7101a52c 100644
--- a/GitTfs/Commands/Init.cs
+++ b/GitTfs/Commands/Init.cs
@@ -101,6 +101,8 @@ namespace Sep.Git.Tfs.Commands
                 }
             }
 
+            globals.Repository.SetConfig(GitTfsConstants.IgnoreBranches, false.ToString());
+
         }
 
         private string[] BuildInitCommand()
diff --git a/GitTfs/Core/GitRepository.cs b/GitTfs/Core/GitRepository.cs
index 46134681..505fc478 100644
--- a/GitTfs/Core/GitRepository.cs
+++ b/GitTfs/Core/GitRepository.cs
@@ -105,6 +105,7 @@ namespace Sep.Git.Tfs.Core
                 return defaultValue;
             }
         }
+
         public void SetConfig(string key, string value)
         {
             _repository.Config.Set<string>(key, value, ConfigurationLevel.Local);