diff --git a/lib/repository.js b/lib/repository.js
@@ -665,17 +665,18 @@ Repository.prototype.mergeBranches = function(to, from, signature) {
   signature = signature || repo.defaultSignature();
 
   return Promise.all([
-    repo.getBranch(to),
-    repo.getBranch(from)
-  ]).then(function(branches) {
-    toBranch = branches[0];
-    fromBranch = branches[1];
+      repo.getBranch(to),
+      repo.getBranch(from)
+  ]).then(function(objects) {
+    toBranch = objects[0];
+    fromBranch = objects[1];
 
     return Promise.all([
       repo.getBranchCommit(toBranch),
       repo.getBranchCommit(fromBranch)
     ]);
-  }).then(function(branchCommits) {
+  })
+  .then(function(branchCommits) {
     var toCommitOid = branchCommits[0].toString();
     var fromCommitOid = branchCommits[1].toString();
 
@@ -694,12 +695,24 @@ Repository.prototype.mergeBranches = function(to, from, signature) {
           " to branch " +
           fromBranch.shorthand();
 
-        return toBranch.setTarget(
-          fromCommitOid,
-          signature,
-          message)
+        return branchCommits[1].getTree()
+        .then(function(tree) {
+          if (toBranch.isHead()) {
+            // Checkout the tree if we're on the branch
+            var opts = {
+              checkoutStrategy: NodeGit.Checkout.STRATEGY.SAFE_CREATE
+            };
+            return NodeGit.Checkout.tree(repo, tree, opts);
+          }
+        })
         .then(function() {
-          return fromCommitOid;
+          return toBranch.setTarget(
+            fromCommitOid,
+            signature,
+            message)
+          .then(function() {
+            return fromCommitOid;
+          });
         });
       }
       else {
@@ -804,24 +817,29 @@ Repository.prototype.getStatusExt = function(opts) {
  */
 Repository.prototype.checkoutBranch = function(branch, opts) {
   var repo = this;
-
+  var reference;
   opts = opts || {};
-  opts.checkoutStrategy = opts.checkoutStrategy || Checkout.STRATEGY.SAFE;
-
+  opts.checkoutStrategy = opts.checkoutStrategy ||
+    Checkout.STRATEGY.SAFE_CREATE;
   return repo.getReference(branch)
   .then(function(ref) {
     if (!ref.isBranch()) {
       return false;
     }
-
-    var name = ref.name();
-
+    reference = ref;
+    return repo.getBranchCommit(ref.name());
+  })
+  .then(function(commit) {
+    return commit.getTree();
+  })
+  .then(function(tree) {
+    return Checkout.tree(repo, tree, opts);
+  })
+  .then(function() {
+    var name = reference.name();
     return repo.setHead(name,
       repo.defaultSignature(),
       "Switch HEAD to " + name);
-  })
-  .then(function() {
-    return Checkout.head(repo, opts);
   });
 };
 

diff --git a/test/tests/checkout.js b/test/tests/checkout.js
@@ -86,18 +86,20 @@ describe("Checkout", function() {
   it("can checkout a branch", function() {
     var test = this;
 
-    return test.repository.checkoutBranch(checkoutBranchName, {
-      checkoutStrategy: Checkout.STRATEGY.FORCE
-    })
+    return test.repository.checkoutBranch(checkoutBranchName)
     .then(function() {
       var packageContent = fse.readFileSync(packageJsonPath, "utf-8");
 
       assert.ok(!~packageContent.indexOf("\"ejs\": \"~1.0.0\","));
     })
     .then(function() {
-      return test.repository.checkoutBranch("master", {
-        checkoutStrategy: Checkout.STRATEGY.FORCE
-      });
+      return test.repository.getStatus();
+    })
+    .then(function(statuses) {
+      assert.equal(statuses.length, 0);
+    })
+    .then(function() {
+      return test.repository.checkoutBranch("master");
     })
     .then(function() {
       var packageContent = fse.readFileSync(packageJsonPath, "utf-8");

diff --git a/test/tests/merge.js b/test/tests/merge.js
@@ -214,6 +214,10 @@ describe("Merge", function() {
         theirCommit = commit;
       });
     })
+    .then(function() {
+      var opts = {checkoutStrategy: NodeGit.Checkout.STRATEGY.FORCE};
+      return repository.checkoutBranch(ourBranchName, opts);
+    })
     .then(function() {
       return repository.mergeBranches(
         ourBranchName,
@@ -228,6 +232,13 @@ describe("Merge", function() {
         .then(function(branchCommit) {
           assert.equal(oid.toString(), branchCommit.toString());
         });
+    })
+    .then(function() {
+      return repository.getStatus();
+    })
+    .then(function(statuses) {
+      // make sure we didn't change the index
+      assert.equal(statuses.length, 0);
     });
   });