diff --git a/testing/fixtures.py b/testing/fixtures.py
index 36c7400c..fdf651e8 100644
--- a/testing/fixtures.py
+++ b/testing/fixtures.py
@@ -94,18 +94,24 @@ def make_config_from_repo(repo_path, sha=None, hooks=None, check=True):
         return config
 
 
-def write_config(directory, config):
+def read_config(directory, config_file=C.CONFIG_FILE):
+    config_path = os.path.join(directory, config_file)
+    config = ordered_load(io.open(config_path).read())
+    return config
+
+
+def write_config(directory, config, config_file=C.CONFIG_FILE):
     if type(config) is not list:
         assert type(config) is OrderedDict
         config = [config]
-    with io.open(os.path.join(directory, C.CONFIG_FILE), 'w') as config_file:
-        config_file.write(ordered_dump(config, **C.YAML_DUMP_KWARGS))
+    with io.open(os.path.join(directory, config_file), 'w') as outfile:
+        outfile.write(ordered_dump(config, **C.YAML_DUMP_KWARGS))
 
 
-def add_config_to_repo(git_path, config):
-    write_config(git_path, config)
+def add_config_to_repo(git_path, config, config_file=C.CONFIG_FILE):
+    write_config(git_path, config, config_file=config_file)
     with cwd(git_path):
-        cmd_output('git', 'add', C.CONFIG_FILE)
+        cmd_output('git', 'add', config_file)
         cmd_output('git', 'commit', '-m', 'Add hooks config')
     return git_path
 
diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index a7a651ed..86d0ecd4 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -24,6 +24,7 @@ from testing.auto_namedtuple import auto_namedtuple
 from testing.fixtures import add_config_to_repo
 from testing.fixtures import make_consuming_repo
 from testing.fixtures import modify_config
+from testing.fixtures import read_config
 from testing.util import cmd_output_mocked_pre_commit_home
 
 
@@ -74,19 +75,20 @@ def _get_opts(
     )
 
 
-def _do_run(cap_out, repo, args, environ={}):
-    runner = Runner(repo, C.CONFIG_FILE)
+def _do_run(cap_out, repo, args, environ={}, config_file=C.CONFIG_FILE):
+    runner = Runner(repo, config_file)
     with cwd(runner.git_root):  # replicates Runner.create behaviour
         ret = run(runner, args, environ=environ)
     printed = cap_out.get_bytes()
     return ret, printed
 
 
-def _test_run(cap_out, repo, opts, expected_outputs, expected_ret, stage):
+def _test_run(cap_out, repo, opts, expected_outputs, expected_ret, stage,
+              config_file=C.CONFIG_FILE):
     if stage:
         stage_a_file()
     args = _get_opts(**opts)
-    ret, printed = _do_run(cap_out, repo, args)
+    ret, printed = _do_run(cap_out, repo, args, config_file=config_file)
 
     assert ret == expected_ret, (ret, expected_ret, printed)
     for expected_output_part in expected_outputs:
@@ -205,6 +207,26 @@ def test_always_run(
     )
 
 
+def test_always_run_alt_config(
+        cap_out, repo_with_passing_hook, mock_out_store_directory,
+):
+    repo_root = '.'
+    config = read_config(repo_root)
+    config[0]['hooks'][0]['always_run'] = True
+    alt_config_file = 'alternate_config.yaml'
+    add_config_to_repo(repo_root, config, config_file=alt_config_file)
+
+    _test_run(
+        cap_out,
+        repo_with_passing_hook,
+        {},
+        (b'Bash hook', b'Passed'),
+        0,
+        stage=False,
+        config_file=alt_config_file
+    )
+
+
 @pytest.mark.parametrize(
     ('origin', 'source', 'expect_failure'),
     (
diff --git a/tests/runner_test.py b/tests/runner_test.py
index f93cb360..9039e573 100644
--- a/tests/runner_test.py
+++ b/tests/runner_test.py
@@ -79,6 +79,38 @@ def test_local_hooks(tempdir_factory, mock_out_store_directory):
     assert len(runner.repositories[0].hooks) == 2
 
 
+def test_local_hooks_alt_config(tempdir_factory, mock_out_store_directory):
+    config = OrderedDict((
+        ('repo', 'local'),
+        ('hooks', (OrderedDict((
+            ('id', 'arg-per-line'),
+            ('name', 'Args per line hook'),
+            ('entry', 'bin/hook.sh'),
+            ('language', 'script'),
+            ('files', ''),
+            ('args', ['hello', 'world']),
+        )), OrderedDict((
+            ('id', 'ugly-format-json'),
+            ('name', 'Ugly format json'),
+            ('entry', 'ugly-format-json'),
+            ('language', 'python'),
+            ('files', ''),
+        )), OrderedDict((
+            ('id', 'do_not_commit'),
+            ('name', 'Block if "DO NOT COMMIT" is found'),
+            ('entry', 'DO NOT COMMIT'),
+            ('language', 'pcre'),
+            ('files', '^(.*)$'),
+        ))))
+    ))
+    git_path = git_dir(tempdir_factory)
+    alt_config_file = 'alternate_config.yaml'
+    add_config_to_repo(git_path, config, config_file=alt_config_file)
+    runner = Runner(git_path, alt_config_file)
+    assert len(runner.repositories) == 1
+    assert len(runner.repositories[0].hooks) == 3
+
+
 def test_pre_commit_path(in_tmpdir):
     path = os.path.join('foo', 'bar')
     cmd_output('git', 'init', path)