diff --git a/kallithea/bin/kallithea_cli_base.py b/kallithea/bin/kallithea_cli_base.py
--- a/kallithea/bin/kallithea_cli_base.py
+++ b/kallithea/bin/kallithea_cli_base.py
@@ -13,8 +13,10 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import click
+import cStringIO
 import functools
 import os
+import re
 import sys
 
 import kallithea
@@ -31,6 +33,19 @@ import paste.deploy
 kallithea_cli_path = sys.argv[0]
 
 
+def read_config(ini_file_name, strip_section_prefix):
+    """Read ini_file_name content, and for all sections like '[X:Y]' where X is
+    strip_section_prefix, replace the section name with '[Y]'."""
+
+    def repl(m):
+        if m.group(1) == strip_section_prefix:
+            return '[%s]' % m.group(2)
+        return m.group(0)
+
+    with open(ini_file_name) as f:
+        return re.sub(r'^\[([^:]+):(.*)]', repl, f.read(), flags=re.MULTILINE)
+
+
 # This placeholder is the main entry point for the kallithea-cli command
 @click.group(context_settings=dict(help_option_names=['-h', '--help']))
 def cli():
@@ -55,7 +70,8 @@ def register_command(config_file=False, 
             def runtime_wrapper(config_file, *args, **kwargs):
                 path_to_ini_file = os.path.realpath(config_file)
                 kallithea.CONFIG = paste.deploy.appconfig('config:' + path_to_ini_file)
-                logging.config.fileConfig(path_to_ini_file)
+                config_bytes = read_config(path_to_ini_file, strip_section_prefix=annotated.__name__)
+                logging.config.fileConfig(cStringIO.StringIO(config_bytes))
                 if config_file_initialize_app:
                     kallithea.config.middleware.make_app_without_logging(kallithea.CONFIG.global_conf, **kallithea.CONFIG.local_conf)
                     kallithea.lib.utils.setup_cache_regions(kallithea.CONFIG)