diff --git a/ctapipe/core/tests/test_tool.py b/ctapipe/core/tests/test_tool.py
index 8db62479be1..a65ecf8344a 100644
--- a/ctapipe/core/tests/test_tool.py
+++ b/ctapipe/core/tests/test_tool.py
@@ -426,3 +426,38 @@ def start(self):
     assert run_tool(tool, raises=False) == 1
     assert tool.manager.enter_called
     assert tool.manager.exit_called
+
+
+def test_activity(tmp_path):
+    """check that the config is correctly in the provenance"""
+
+    class MyTool(Tool):
+        name = "test_prov_log"
+        description = "test"
+        userparam = Float(5.0, help="parameter").tag(config=True)
+
+    tool = MyTool()
+
+    config_path = tmp_path / "config.json"
+    config_path.write_text(json.dumps({"MyTool": {"userparam": 10.0}}))
+    provenance_path = tmp_path / "provenance.json"
+
+    run_tool(
+        tool,
+        [
+            "--config",
+            str(config_path),
+            f"--provenance-log={provenance_path}",
+        ],
+    )
+
+    activities = json.loads(tool.provenance_log.read_text())
+    # provlog contains all activities from all tests, last one is the tool we just ran
+    provlog = activities[-1]
+    assert provlog["activity_name"] == MyTool.name
+
+    # test config file is in inputs, regression test for #2313
+    inputs = provlog["input"]
+    assert len(inputs) == 1
+    assert inputs[0]["role"] == "Tool Configuration"
+    assert inputs[0]["url"] == str(config_path)
diff --git a/ctapipe/core/tool.py b/ctapipe/core/tool.py
index 56de387a271..e39dcaff89b 100644
--- a/ctapipe/core/tool.py
+++ b/ctapipe/core/tool.py
@@ -405,11 +405,14 @@ def run(self, argv=None, raises=False):
 
         with self._exit_stack:
             try:
-                self.initialize(argv)
                 self.log.info(f"Starting: {self.name}")
                 Provenance().start_activity(self.name)
+
+                self.initialize(argv)
+
                 self.setup()
                 self.is_setup = True
+
                 self.log.debug(f"CONFIG: {self.get_current_config()}")
                 Provenance().add_config(self.get_current_config())
 
diff --git a/docs/changes/2312.bugfix.rst b/docs/changes/2312.bugfix.rst
new file mode 100644
index 00000000000..cdcf85d1e7c
--- /dev/null
+++ b/docs/changes/2312.bugfix.rst
@@ -0,0 +1 @@
+Fix for config files not being included as inputs in provenance log.