diff --git a/ckan/lib/config_tool.py b/ckan/lib/config_tool.py
index 5895d531db8..6cf375ad0d6 100644
--- a/ckan/lib/config_tool.py
+++ b/ckan/lib/config_tool.py
@@ -1,6 +1,7 @@
 # encoding: utf-8
 
 from __future__ import print_function
+import six
 import re
 
 INSERT_NEW_SECTIONS_BEFORE_SECTION = 'app:main'
@@ -23,7 +24,7 @@ def config_edit_using_merge_file(config_filepath, merge_config_filepath):
     '''
     # Read and parse the merge config filepath
     with open(merge_config_filepath, 'rb') as f:
-        input_lines = [line.rstrip('\n') for line in f]
+        input_lines = [six.ensure_str(line).rstrip('\n') for line in f]
     desired_options_dict = parse_config(input_lines)
     desired_options = desired_options_dict.values()
     # Make the changes
@@ -34,7 +35,7 @@ def config_edit(config_filepath, desired_options, edit=False):
     '''Writes the desired_options to the config file.'''
     # Read and parse the existing config file
     with open(config_filepath, 'rb') as f:
-        input_lines = [line.rstrip('\n') for line in f]
+        input_lines = [six.ensure_str(line).rstrip('\n') for line in f]
     existing_options_dict = parse_config(input_lines)
     existing_options = existing_options_dict.values()
 
@@ -45,7 +46,7 @@ def config_edit(config_filepath, desired_options, edit=False):
     # write the file with the changes
     output = make_changes(input_lines, new_sections, changes)
     with open(config_filepath, 'wb') as f:
-        f.write('\n'.join(output) + '\n')
+        f.write(six.ensure_binary('\n'.join(output) + '\n'))
 
 
 def parse_option_string(section, option_string, raise_on_error=False):
diff --git a/ckan/tests/cli/test_config_tool.py b/ckan/tests/cli/test_config_tool.py
index d7d22bd8a63..876d11c8317 100644
--- a/ckan/tests/cli/test_config_tool.py
+++ b/ckan/tests/cli/test_config_tool.py
@@ -34,7 +34,9 @@ def test_config_unset_debug(cli, config_file):
     assert _parse(config_file).get(u'app:main', u'debug') == u'true'
     result = cli.invoke(
         ckan,
-        [u'config-tool', str(config_file), u'debug=false'])
+        [u'config-tool', str(config_file), u'debug=false']
+
+    )
     assert not result.exit_code
     assert _parse(config_file).get(u'app:main', u'debug') == u'false'
 
diff --git a/ckan/tests/helpers.py b/ckan/tests/helpers.py
index 077ce2faf0a..889a17194ee 100644
--- a/ckan/tests/helpers.py
+++ b/ckan/tests/helpers.py
@@ -30,6 +30,7 @@
 
 from flask.testing import Client as FlaskClient
 from flask.wrappers import Response
+from click.testing import CliRunner
 import pytest
 import mock
 import rq
@@ -172,6 +173,14 @@ def body_contains(res, content):
     return content in body
 
 
+class CKANCliRunner(CliRunner):
+    def invoke(self, *args, **kwargs):
+        # prevent cli runner from str/bytes exceptions
+        kwargs.setdefault(u'complete_var', u'_CKAN_COMPLETE')
+        return super(CKANCliRunner, self).invoke(*args, **kwargs)
+
+
+
 class CKANResponse(Response):
     @property
     def body(self):
diff --git a/ckan/tests/pytest_ckan/fixtures.py b/ckan/tests/pytest_ckan/fixtures.py
index ae23720107b..1e2626848da 100644
--- a/ckan/tests/pytest_ckan/fixtures.py
+++ b/ckan/tests/pytest_ckan/fixtures.py
@@ -28,16 +28,19 @@
 
 """
 
-import pytest
+import functools
+import smtplib
+
 
-from click.testing import CliRunner
+import pytest
 import six
 import mock
-import smtplib
+import rq
+
 import ckan.tests.helpers as test_helpers
 import ckan.plugins
 import ckan.lib.search as search
-import rq
+
 from ckan.common import config
 
 
@@ -110,8 +113,8 @@ def test_dataset_search(self, app):
 def cli(ckan_config):
     """Provides object for invoking CLI commands from tests.
 
-    This is pure `click.testing.CliRunner`, so all examples from
-    `Click docs
+    This is subclass of `click.testing.CliRunner`, so all examples
+    from `Click docs
     <https://click.palletsprojects.com/en/master/testing/>`_ are valid
     for it.
 
@@ -119,7 +122,7 @@ def cli(ckan_config):
     env = {
         u'CKAN_INI': ckan_config[u'__file__']
     }
-    return CliRunner(env=env)
+    return test_helpers.CKANCliRunner(env=env)
 
 
 @pytest.fixture(scope=u"session")