diff --git a/bookwyrm/management/commands/deduplicate_book_data.py b/bookwyrm/management/commands/deduplicate_book_data.py
index 5ca8496b0..4519d2cff 100644
--- a/bookwyrm/management/commands/deduplicate_book_data.py
+++ b/bookwyrm/management/commands/deduplicate_book_data.py
@@ -1,7 +1,7 @@
 """ PROCEED WITH CAUTION: uses deduplication fields to permanently
 merge book data objects """
 from django.core.management.base import BaseCommand
-from django.db.models import Count
+from django.db.models import Count, ManyToManyField
 from bookwyrm import models
 
 
@@ -12,6 +12,16 @@ def update_related(canonical, obj):
         (r.remote_field.name, r.related_model) for r in canonical._meta.related_objects
     ]
     for (related_field, related_model) in related_models:
+        # Skip the ManyToMany fields that aren’t auto-created. These
+        # should have a corresponding OneToMany field in the model for
+        # the linking table anyway. If we update it through that model
+        # instead then we won’t lose the extra fields in the linking
+        # table.
+        related_field_obj = related_model._meta.get_field(related_field)
+        if isinstance(related_field_obj, ManyToManyField):
+            through = related_field_obj.remote_field.through
+            if not through._meta.auto_created:
+                continue
         related_objs = related_model.objects.filter(**{related_field: obj})
         for related_obj in related_objs:
             print("replacing in", related_model.__name__, related_field, related_obj.id)