diff --git a/gravity/state.py b/gravity/state.py
index 992fbc1..bcb1af9 100644
--- a/gravity/state.py
+++ b/gravity/state.py
@@ -11,6 +11,9 @@
 from gravity.util import AttributeDict
 
 
+GALAXY_YML_SAMPLE_PATH = "lib/galaxy/config/sample/galaxy.yml.sample"
+
+
 class GracefulMethod(enum.Enum):
     DEFAULT = 0
     SIGHUP = 1
@@ -144,6 +147,11 @@ def __init__(self, *args, **kwargs):
             for config_file, config_dict in self[key].items():
                 # resolve path, so we always deal with absolute and symlink-resolved paths
                 config_file = os.path.realpath(config_file)
+                if config_file.endswith(GALAXY_YML_SAMPLE_PATH):
+                    root_dir = config_dict['attribs']['galaxy_root']
+                    non_sample_path = os.path.join(root_dir, 'config', 'galaxy.yml')
+                    if os.path.exists(non_sample_path):
+                        config_file = non_sample_path
                 normalized_state[key][config_file] = ConfigFile(config_dict)
         self.update(normalized_state)
 
diff --git a/tests/conftest.py b/tests/conftest.py
index f11099d..d49e027 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -46,7 +46,7 @@ def galaxy_root_dir(galaxy_git_dir, tmpdir_factory):
 
 @pytest.fixture()
 def galaxy_yml(galaxy_root_dir):
-    config = galaxy_root_dir / 'config' / 'galaxy.yml'
+    config = galaxy_root_dir / 'config' / 'galaxy123.yml'
     sample_config = galaxy_root_dir / 'config' / 'galaxy.yml.sample'
     sample_config.copy(config)
     try:
diff --git a/tests/test_config_manager.py b/tests/test_config_manager.py
index 60f23c4..41818ca 100644
--- a/tests/test_config_manager.py
+++ b/tests/test_config_manager.py
@@ -65,7 +65,7 @@ def test_deregister(galaxy_yml, default_config_manager):
 def test_rename(galaxy_root_dir, state_dir, default_config_manager):
     galaxy_yml_sample = galaxy_root_dir / "config" / "galaxy.yml.sample"
     default_config_manager.add([str(galaxy_yml_sample)])
-    galaxy_yml = galaxy_root_dir / "config" / "galaxy.yml"
+    galaxy_yml = galaxy_root_dir / "config" / "galaxy123.yml"
     galaxy_yml_sample.copy(galaxy_yml)
     assert default_config_manager.is_registered(str(galaxy_yml_sample.realpath()))
     assert not default_config_manager.is_registered(str(galaxy_yml))
@@ -79,3 +79,12 @@ def test_auto_register(galaxy_yml, default_config_manager, monkeypatch):
     assert not default_config_manager.is_registered(str(galaxy_yml))
     default_config_manager.auto_register()
     assert default_config_manager.is_registered(str(galaxy_yml))
+
+
+def test_register_sample_update_to_non_sample(galaxy_root_dir, state_dir, default_config_manager):
+    galaxy_yml_sample = galaxy_root_dir / "config" / "galaxy.yml.sample"
+    default_config_manager.add([str(galaxy_yml_sample)])
+    galaxy_yml = galaxy_root_dir / "config" / "galaxy.yml"
+    galaxy_yml_sample.copy(galaxy_yml)
+    default_config_manager.instance_count == 1
+    assert default_config_manager.get_registered_config(str(galaxy_yml))
diff --git a/tests/test_operations.py b/tests/test_operations.py
index e97ff22..f13865e 100644
--- a/tests/test_operations.py
+++ b/tests/test_operations.py
@@ -1,6 +1,7 @@
 import json
 import re
 import time
+from pathlib import Path
 
 import requests
 from click.testing import CliRunner
@@ -121,7 +122,8 @@ def test_cmd_show_config_does_not_exist(state_dir, galaxy_yml):
     assert "Registered config files are:" not in result.output
     assert f'To register this config file run "galaxyctl register {str(galaxy_yml)}"' in result.output
     # register the sample file, but ask for galaxy.yml
-    result = runner.invoke(galaxyctl, ['--state-dir', state_dir, 'register', str(galaxy_yml + '.sample')])
+    sample_file = Path(galaxy_yml).parent / 'galaxy.yml.sample'
+    result = runner.invoke(galaxyctl, ['--state-dir', state_dir, 'register', str(sample_file)])
     assert result.exit_code == 0, result.output
     result = runner.invoke(galaxyctl, ['--state-dir', state_dir, 'show', str(galaxy_yml)])
     assert result.exit_code == 1
diff --git a/tests/test_process_manager.py b/tests/test_process_manager.py
index 26d3a46..fbd76c2 100644
--- a/tests/test_process_manager.py
+++ b/tests/test_process_manager.py
@@ -107,10 +107,10 @@ def test_static_handlers(default_config_manager, galaxy_yml, job_conf):
         instance_conf_dir = Path(default_config_manager.state_dir) / 'supervisor' / 'supervisord.conf.d' / '_default_.d'
         handler0_config_path = instance_conf_dir / 'galaxy_standalone_handler0.conf'
         assert handler0_config_path.exists()
-        assert 'galaxy.yml --server-name=handler0 --pid-file=' in handler0_config_path.open().read()
+        assert f'{str(galaxy_yml)} --server-name=handler0 --pid-file=' in handler0_config_path.open().read()
         handler1_config_path = instance_conf_dir / 'galaxy_standalone_handler1.conf'
         assert handler1_config_path.exists()
-        assert 'galaxy.yml --server-name=handler1 --pid-file=' in handler1_config_path.open().read()
+        assert f'{str(galaxy_yml)} --server-name=handler1 --pid-file=' in handler1_config_path.open().read()
 
 
 def test_gxit_handler(default_config_manager, galaxy_yml, gxit_config):