diff --git a/beets/dbcore/db.py b/beets/dbcore/db.py
index e66f4548bf..f002146ed9 100755
--- a/beets/dbcore/db.py
+++ b/beets/dbcore/db.py
@@ -586,10 +586,19 @@ def store(self, fields: Iterable[str] | None = None) -> None:
         if fields is None:
             fields = self._fields
 
+        # Separate the requested fields into fixed (real columns in the main
+        # table) and flexible (persisted via ``_flex_table``). Callers such as
+        # ``beet update`` may pass a flex attribute through ``fields=`` -- for
+        # example, when a plugin registers it via both ``item_types`` and
+        # ``add_media_field``. Treating a flex attribute as a column here used
+        # to build ``UPDATE <table> SET <flex>=?`` and crash with
+        # ``sqlite3.OperationalError: no such column: <flex>`` (see #5580).
+        column_fields = [f for f in fields if f in self._fields]
+
         # Build assignments for query.
         assignments = []
         subvars: list[SQLiteType] = []
-        for key in fields:
+        for key in column_fields:
             if key != "id" and key in self._dirty:
                 self._dirty.remove(key)
                 assignments.append(f"{key}=?")
diff --git a/docs/changelog.rst b/docs/changelog.rst
index 096a35a6db..84fc808d1b 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -58,6 +58,13 @@ New features
 Bug fixes
 ~~~~~~~~~
 
+- Fixed a ``sqlite3.OperationalError: no such column`` crash in ``Model.store``
+  when a field passed via the ``fields`` argument was a flexible attribute
+  rather than a fixed column. The fields set is now filtered to fixed columns
+  for the main-table ``UPDATE``; flexible attributes continue to be persisted
+  via the ``_flex_table`` path. This affected plugins that register fields via
+  both ``item_types`` and ``add_media_field`` and were later updated with ``beet
+  update``. :bug:`5580`
 - :doc:`plugins/edit`: Preserve missing album art paths when editing album
   metadata, instead of turning ``artpath: null`` into a path ending in ``None``.
   :bug:`2438`
diff --git a/test/dbcore/test_db.py b/test/dbcore/test_db.py
index 829919847a..fb33b49e33 100644
--- a/test/dbcore/test_db.py
+++ b/test/dbcore/test_db.py
@@ -281,6 +281,27 @@ def test_store_and_retrieve_flexattr(self):
         other_model = self.db._get(ModelFixture1, model.id)
         assert other_model.foo == "bar"
 
+    def test_store_with_flex_field_in_fields_argument(self):
+        """A flex attribute passed via ``fields=`` must not crash.
+
+        Regression test for #5580: when a plugin registers a typed flex
+        attribute (via ``item_types``) and a caller such as ``beet update``
+        passes its name through ``fields=`` to ``Model.store()``, the store
+        loop used to build ``UPDATE <table> SET <flex_field>=?`` and crash
+        with ``sqlite3.OperationalError: no such column: <flex_field>``.
+        Flex attributes have no column in the main table; they live in the
+        ``_flex_table`` and must be persisted via the INSERT path.
+        """
+        model = ModelFixture1()
+        model.add(self.db)
+        model.field_one = 42
+        model.some_float_field = 1.5
+        model.store(fields=["field_one", "some_float_field"])
+
+        other_model = self.db._get(ModelFixture1, model.id)
+        assert other_model.field_one == 42
+        assert other_model.some_float_field == 1.5
+
     def test_delete_flexattr(self):
         model = ModelFixture1()
         model["foo"] = "bar"