diff --git a/beets/dbcore/db.py b/beets/dbcore/db.py
index e66f4548bf..a16ad582e6 100755
--- a/beets/dbcore/db.py
+++ b/beets/dbcore/db.py
@@ -590,7 +590,7 @@ def store(self, fields: Iterable[str] | None = None) -> None:
         assignments = []
         subvars: list[SQLiteType] = []
         for key in fields:
-            if key != "id" and key in self._dirty:
+            if key != "id" and key in self._fields and key in self._dirty:
                 self._dirty.remove(key)
                 assignments.append(f"{key}=?")
                 value = self._type(key).to_sql(self[key])
diff --git a/docs/changelog.rst b/docs/changelog.rst
index 30fbfa3e60..7fec5df5c9 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -114,6 +114,8 @@ Bug fixes
   valid date/time string" error instead of crashing with an uncaught
   ``KeyError``. A ``|`` was being accepted as a relative-date unit due to a
   regular expression character-class typo.
+- ``beet update`` no longer crashes when a plugin-added media field is stored as
+  a flexible attribute. :bug:`5580`
 
 ..
     For plugin developers
diff --git a/test/dbcore/test_db.py b/test/dbcore/test_db.py
index 829919847a..353a30ae3b 100644
--- a/test/dbcore/test_db.py
+++ b/test/dbcore/test_db.py
@@ -281,6 +281,15 @@ def test_store_and_retrieve_flexattr(self):
         other_model = self.db._get(ModelFixture1, model.id)
         assert other_model.foo == "bar"
 
+    def test_store_flexattr_in_fields(self):
+        model = ModelFixture1()
+        model.add(self.db)
+        model.foo = "bar"
+        model.store(fields=["foo"])
+
+        other_model = self.db._get(ModelFixture1, model.id)
+        assert other_model.foo == "bar"
+
     def test_delete_flexattr(self):
         model = ModelFixture1()
         model["foo"] = "bar"
diff --git a/test/ui/commands/test_update.py b/test/ui/commands/test_update.py
index 1b7d368346..aa98508da2 100644
--- a/test/ui/commands/test_update.py
+++ b/test/ui/commands/test_update.py
@@ -1,8 +1,10 @@
 import os
 
+import mediafile
 from mediafile import MediaFile
 
 from beets import library
+from beets.plugins import BeetsPlugin
 from beets.test import _common
 from beets.test.helper import BeetsTestCase, IOMixin
 from beets.ui.commands.update import update_items
@@ -84,6 +86,29 @@ def test_modified_metadata_detected(self):
         item = self.lib.items().get()
         assert item.title == "differentTitle"
 
+    def test_modified_plugin_media_field_detected(self):
+        plugin = BeetsPlugin()
+        plugin.add_media_field(
+            "customtag",
+            mediafile.MediaField(
+                mediafile.MP3DescStorageStyle("customtag"),
+                mediafile.StorageStyle("customtag"),
+            ),
+        )
+
+        try:
+            mf = MediaFile(syspath(self.i.path))
+            mf.customtag = "F#"
+            mf.save()
+
+            self._update()
+
+            item = self.lib.get_item(self.i.id)
+            assert item["customtag"] == "F#"
+        finally:
+            delattr(mediafile.MediaFile, "customtag")
+            library.Item._media_fields.remove("customtag")
+
     def test_modified_metadata_moved(self):
         mf = MediaFile(syspath(self.i.path))
         mf.title = "differentTitle"