diff --git a/.travis.yml b/.travis.yml
index 94e13f47..40863080 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -34,7 +34,7 @@ script:
       python -m doctr deploy --sync .;
       python -m doctr deploy --sync --gh-pages-docs docs;
       python -m doctr deploy --sync --no-require-master  --built-docs docs/_build/html "docs-$TRAVIS_BRANCH";
-      python -m doctr deploy --no-require-master  --command "echo test; ls" docs;
+      python -m doctr deploy --no-require-master  --command "echo test; ls; touch docs/_build/html/test" docs;
     fi
   - if [[ "${TESTS}" == "true" ]]; then
       pyflakes doctr;
diff --git a/doctr/__init__.py b/doctr/__init__.py
index 5245b4e6..38687811 100644
--- a/doctr/__init__.py
+++ b/doctr/__init__.py
@@ -2,16 +2,18 @@
     generate_GitHub_token, upload_GitHub_deploy_key, generate_ssh_key,
     check_repo_exists)
 from .travis import (decrypt_file, setup_deploy_key, get_token, run,
-    setup_GitHub_push, deploy_branch_exists, create_deploy_branch, sync_from_log,
-    commit_docs, push_docs, get_current_repo, find_sphinx_build_dir)
+    setup_GitHub_push, checkout_deploy_branch, deploy_branch_exists,
+    create_deploy_branch, copy_to_tmp, sync_from_log, commit_docs, push_docs,
+    get_current_repo, find_sphinx_build_dir)
 
 __all__ = [
     'encrypt_variable', 'encrypt_file', 'GitHub_post',
     'generate_GitHub_token', 'upload_GitHub_deploy_key', 'generate_ssh_key',
     'check_repo_exists',
 
-    'decrypt_file', 'setup_deploy_key', 'get_token', 'run', 'setup_GitHub_push', 'deploy_branch_exists',
-    'create_deploy_branch', 'sync_from_log', 'commit_docs', 'push_docs', 'get_current_repo', 'find_sphinx_build_dir'
+    'decrypt_file', 'setup_deploy_key', 'get_token', 'run',
+    'setup_GitHub_push', 'checkout_deploy_branch', 'deploy_branch_exists',
+    'create_deploy_branch', 'copy_to_tmp', 'sync_from_log', 'commit_docs', 'push_docs', 'get_current_repo', 'find_sphinx_build_dir'
 ]
 
 from ._version import get_versions
diff --git a/doctr/__main__.py b/doctr/__main__.py
index 22871182..e734bc18 100644
--- a/doctr/__main__.py
+++ b/doctr/__main__.py
@@ -36,7 +36,8 @@
 from .local import (generate_GitHub_token, encrypt_variable, encrypt_file,
     upload_GitHub_deploy_key, generate_ssh_key, check_repo_exists, GitHub_login)
 from .travis import (setup_GitHub_push, commit_docs, push_docs,
-    get_current_repo, sync_from_log, find_sphinx_build_dir, run, get_travis_branch)
+    get_current_repo, sync_from_log, find_sphinx_build_dir, run,
+    get_travis_branch, copy_to_tmp, checkout_deploy_branch)
 from . import __version__
 
 def make_parser_with_config_adder(parser, config):
@@ -152,6 +153,9 @@ def get_parser(config=None):
         conjunction with the --command flag, for instance, if the command syncs
         the files for you. Any files you wish to commit should be added to the
         index.""")
+    deploy_parser.add_argument('--no-temp-dir', dest='temp_dir',
+        action='store_false', default=True, help="""Don't copy the
+        --built-docs directory to a temporary directory.""")
     deploy_parser_add_argument('--no-push', dest='push', action='store_false',
         default=True, help="Run all the steps except the last push step. "
         "Useful for debugging")
@@ -161,6 +165,7 @@ def get_parser(config=None):
         the first argument to 'doctr deploy'. This flag is kept for backwards
         compatibility.""")
 
+
     if config:
         print('Warning, The following options in `.travis.yml` were not recognized:\n%s' % json.dumps(config, indent=2))
 
@@ -249,14 +254,25 @@ def deploy(args, parser):
         branch_whitelist = {'master'} if args.require_master else set(get_travis_branch())
         branch_whitelist.update(set(config.get('branches',set({}))))
 
-        can_push = setup_GitHub_push(deploy_repo, deploy_branch=deploy_branch,
+        canpush = setup_GitHub_push(deploy_repo, deploy_branch=deploy_branch,
                                      auth_type='token' if args.token else 'deploy_key',
                                      full_key_path=args.key_path,
                                      branch_whitelist=branch_whitelist)
 
+        if args.command:
+            run(args.command, shell=True)
+
         if args.sync:
             built_docs = args.built_docs or find_sphinx_build_dir()
+            if args.temp_dir:
+                built_docs = copy_to_tmp(built_docs)
+
+        # Reset in case there are modified files that are tracked in the
+        # dpeloy branch.
+        run(['git', 'reset', '--hard'])
+        checkout_deploy_branch(deploy_branch, canpush=canpush)
 
+        if args.sync:
             log_file = os.path.join(deploy_dir, '.doctr-files')
 
             print("Moving built docs into place")
@@ -266,14 +282,9 @@ def deploy(args, parser):
         else:
             added, removed = [], []
 
-        if args.command:
-            run(['git', 'checkout', get_travis_branch()])
-            run(args.command, shell=True)
-            run(['git', 'checkout', deploy_branch])
-
         changes = commit_docs(added=added, removed=removed)
         if changes:
-            if can_push and args.push:
+            if canpush and args.push:
                 push_docs(deploy_branch)
             else:
                 print("Don't have permission to push. Not trying.")
diff --git a/doctr/travis.py b/doctr/travis.py
index bf073c27..af31bfce 100644
--- a/doctr/travis.py
+++ b/doctr/travis.py
@@ -9,6 +9,8 @@
 import sys
 import glob
 import re
+import pathlib
+import tempfile
 
 from cryptography.fernet import Fernet
 
@@ -218,6 +220,12 @@ def setup_GitHub_push(deploy_repo, auth_type='deploy_key', full_key_path='github
     print("Fetching doctr remote")
     run(['git', 'fetch', 'doctr_remote'])
 
+    return canpush
+
+def checkout_deploy_branch(deploy_branch, canpush=True):
+    """
+    Checkout the deploy branch, creating it if it doesn't exist.
+    """
     #create empty branch with .nojekyll if it doesn't already exist
     new_deploy_branch = create_deploy_branch(deploy_branch, push=canpush)
     print("Checking out {}".format(deploy_branch))
@@ -228,8 +236,6 @@ def setup_GitHub_push(deploy_repo, auth_type='deploy_key', full_key_path='github
         run(['git', 'checkout', '-b', deploy_branch, '--track', 'doctr_remote/{}'.format(deploy_branch)])
     print("Done")
 
-    return canpush
-
 def deploy_branch_exists(deploy_branch):
     """
     Check if there is a remote branch with name specified in ``deploy_branch``.
@@ -294,6 +300,19 @@ def find_sphinx_build_dir():
 # TRAVIS_JOB_NUMBER = os.environ.get("TRAVIS_JOB_NUMBER", '')
 # ACTUAL_TRAVIS_JOB_NUMBER = TRAVIS_JOB_NUMBER.split('.')[1]
 
+def copy_to_tmp(directory):
+    """
+    Copies the contents of directory to a temporary directory, and returns the
+    copied location.
+    """
+    tmp_dir = tempfile.mkdtemp()
+    # Use pathlib because os.path.basename is different depending on whether
+    # the path ends in a /
+    p = pathlib.Path(directory)
+    new_dir = os.path.join(tmp_dir, p.name)
+    shutil.copytree(directory, new_dir)
+    return new_dir
+
 def sync_from_log(src, dst, log_file):
     """
     Sync the files in ``src`` to ``dst``.