diff --git a/changes.d/7365.feat.md b/changes.d/7365.feat.md
index ae8ff76376e..10f6ef284ce 100644
--- a/changes.d/7365.feat.md
+++ b/changes.d/7365.feat.md
@@ -1 +1 @@
-Python warnings raised in users' custom jinja2 filters, globals and tests are now logged.
+Python warnings raised during Jinja2 preprocessing are now logged.
diff --git a/cylc/flow/parsec/fileparse.py b/cylc/flow/parsec/fileparse.py
index 849723136e7..35c4be616ec 100644
--- a/cylc/flow/parsec/fileparse.py
+++ b/cylc/flow/parsec/fileparse.py
@@ -125,6 +125,8 @@
     TEMPLATING_DETECTED: None
 }
 
+_J2_WARN_LOCS = re.compile(rf'jinja2{re.escape(os.sep)}(lexer|runtime)\.py$')
+
 
 def get_cylc_env_vars() -> dict[str, str]:
     """Return a restricted dict of CYLC_ environment variables for templating.
@@ -513,6 +515,13 @@ def read_and_proc(
                 flines = jinja2process(
                     fpath, flines, fdir, template_vars
                 )
+            for w in warns:
+                if _J2_WARN_LOCS.search(w.filename):
+                    # Warning originating from processing of a jinja2 template.
+                    # Unfortunately, we can't know exactly where it originated,
+                    # so just set the config filename and vague line "number":
+                    w.filename = fpath
+                    w.lineno = '<jinja2 template>'  # type: ignore
             if warns:
                 LOG.warning(
                     "The following warnings were raised during Jinja2 "
diff --git a/tests/unit/parsec/test_fileparse.py b/tests/unit/parsec/test_fileparse.py
index d0190246a7c..79caa7439a9 100644
--- a/tests/unit/parsec/test_fileparse.py
+++ b/tests/unit/parsec/test_fileparse.py
@@ -20,6 +20,7 @@
 import re
 import sqlite3
 from tempfile import NamedTemporaryFile
+from textwrap import dedent
 from types import SimpleNamespace
 import warnings
 
@@ -483,6 +484,28 @@ def mock_jinja2process(fpath, *a, **k):
     )
 
 
+def test_read_and_proc_jinja2_warnings_invalid_escape(
+    tmp_path: Path, caplog: pytest.LogCaptureFixture
+):
+    """When a warning comes from a j2 template expression, it should be logged
+    with the cylc config filepath."""
+    (fpath := tmp_path / 'flow.cylc').write_text(
+        dedent(r"""
+            #!jinja2
+            {% from 'warnings' import warn %}
+            {% do warn('Mock warning') %}
+        """).lstrip()
+    )
+    read_and_proc(
+        fpath=str(fpath),
+        viewcfg={'jinja2': True, 'contin': False, 'inline': False},
+    )
+
+    assert (
+        f"{fpath}:<jinja2 template>: UserWarning: Mock warning" in caplog.text
+    )
+
+
 def test_parse_keys_only_singleline():
     with NamedTemporaryFile() as of, NamedTemporaryFile() as tf:
         fpath = tf.name