diff --git a/docs/changelog.rst b/docs/changelog.rst
index c8007e7b..5caa176a 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -14,6 +14,15 @@ Bug fix release.
   backends with a library provider. Previously, it wrongly worked for all
   backends with a playlists provider. (Fixes: :issue:`1257`)
 
+- Core: Respect :confval:`core/cache_dir` and :confval:`core/data_dir` config
+  values added in 1.1.0 when creating the dirs Mopidy need to store data. This
+  should not change the behavior for desktop users running Mopidy. When running
+  Mopidy as a system service installed from a package which sets the core dir
+  configs properly (e.g. Debian and Arch packages), this fix avoids the
+  creation of a couple of directories that should not be used, typically
+  :file:`/var/lib/mopidy/.local` and :file:`/var/lib/mopidy/.cache`. (Fixes:
+  :issue:`1259`)
+
 - Stream: If "file" is present in the :confval:`stream/protocols` config value
   and the :ref:`ext-file` extension is enabled, we exited with an error because
   two extensions claimed the same URI scheme. We now log a warning recommending
diff --git a/mopidy/__main__.py b/mopidy/__main__.py
index ee359268..208d2ff1 100644
--- a/mopidy/__main__.py
+++ b/mopidy/__main__.py
@@ -75,15 +75,16 @@ def main():
 
         args = root_cmd.parse(mopidy_args)
 
-        create_file_structures_and_config(args, extensions_data)
-        check_old_locations()
-
         config, config_errors = config_lib.load(
             args.config_files,
             [d.config_schema for d in extensions_data],
             [d.config_defaults for d in extensions_data],
             args.config_overrides)
 
+        create_core_dirs(config)
+        create_initial_config_file(args, extensions_data)
+        check_old_locations()
+
         verbosity_level = args.base_verbosity_level
         if args.verbosity_level:
             verbosity_level += args.verbosity_level
@@ -166,12 +167,17 @@ def main():
         raise
 
 
-def create_file_structures_and_config(args, extensions_data):
-    path.get_or_create_dir(b'$XDG_DATA_DIR/mopidy')
-    path.get_or_create_dir(b'$XDG_CONFIG_DIR/mopidy')
+def create_core_dirs(config):
+    path.get_or_create_dir(config['core']['cache_dir'])
+    path.get_or_create_dir(config['core']['config_dir'])
+    path.get_or_create_dir(config['core']['data_dir'])
+
+
+def create_initial_config_file(args, extensions_data):
+    """Initialize whatever the last config file is with defaults"""
 
-    # Initialize whatever the last config file is with defaults
     config_file = args.config_files[-1]
+
     if os.path.exists(path.expand_path(config_file)):
         return