diff --git a/django/db/models/expressions.py b/django/db/models/expressions.py
index 203aabeff46..0f9c42009d0 100644
--- a/django/db/models/expressions.py
+++ b/django/db/models/expressions.py
@@ -210,7 +210,7 @@ class BaseExpression(object):
         ])
         return c
 
-    def _prepare(self):
+    def _prepare(self, field):
         """
         Hook used by Field.get_prep_lookup() to do custom preparation.
         """
diff --git a/django/db/models/fields/__init__.py b/django/db/models/fields/__init__.py
index e5c5ca74dfe..56ab438d751 100644
--- a/django/db/models/fields/__init__.py
+++ b/django/db/models/fields/__init__.py
@@ -740,7 +740,7 @@ class Field(RegisterLookupMixin):
         Perform preliminary non-db specific lookup checks and conversions
         """
         if hasattr(value, '_prepare'):
-            return value._prepare()
+            return value._prepare(self)
 
         if lookup_type in {
             'iexact', 'contains', 'icontains',
diff --git a/django/db/models/query.py b/django/db/models/query.py
index 5e2e5d79177..f37ed0f1b65 100644
--- a/django/db/models/query.py
+++ b/django/db/models/query.py
@@ -1108,12 +1108,18 @@ class QuerySet(object):
         for field, objects in other._known_related_objects.items():
             self._known_related_objects.setdefault(field, {}).update(objects)
 
-    def _prepare(self):
+    def _prepare(self, field):
         if self._fields is not None:
             # values() queryset can only be used as nested queries
             # if they are set up to select only a single field.
             if len(self._fields or self.model._meta.concrete_fields) > 1:
                 raise TypeError('Cannot use multi-field values as a filter value.')
+        else:
+            # If the query is used as a subquery for a ForeignKey with non-pk
+            # target field, make sure to select the target field in the subquery.
+            foreign_fields = getattr(field, 'foreign_related_fields', ())
+            if len(foreign_fields) == 1 and not foreign_fields[0].primary_key:
+                return self.values(foreign_fields[0].name)
         return self
 
     def _as_sql(self, connection):
diff --git a/django/db/models/sql/query.py b/django/db/models/sql/query.py
index f9df41392bf..fb3529c2be5 100644
--- a/django/db/models/sql/query.py
+++ b/django/db/models/sql/query.py
@@ -235,7 +235,7 @@ class Query(object):
         memo[id(self)] = result
         return result
 
-    def _prepare(self):
+    def _prepare(self, field):
         return self
 
     def get_compiler(self, using=None, connection=None):
diff --git a/docs/releases/1.9.3.txt b/docs/releases/1.9.3.txt
index 61a92878c7c..e6f200c864c 100644
--- a/docs/releases/1.9.3.txt
+++ b/docs/releases/1.9.3.txt
@@ -21,3 +21,6 @@ Bugfixes
 * Fixed a regression for cases where
   ``ForeignObject.get_extra_descriptor_filter()`` returned a ``Q`` object
   (:ticket:`26153`).
+
+* Fixed regression with an ``__in=qs`` lookup for a ``ForeignKey`` with
+  ``to_field`` set (:ticket:`26196`).
diff --git a/tests/queries/tests.py b/tests/queries/tests.py
index 91ff7bfc8de..e4cb420fda5 100644
--- a/tests/queries/tests.py
+++ b/tests/queries/tests.py
@@ -2416,6 +2416,18 @@ class ToFieldTests(TestCase):
             {lunch, dinner},
         )
 
+    def test_in_subquery(self):
+        apple = Food.objects.create(name="apple")
+        lunch = Eaten.objects.create(food=apple, meal="lunch")
+        self.assertEqual(
+            set(Eaten.objects.filter(food__in=Food.objects.filter(name='apple'))),
+            {lunch}
+        )
+        self.assertEqual(
+            set(Eaten.objects.filter(food__in=Food.objects.filter(name='apple').values('eaten__meal'))),
+            set()
+        )
+
     def test_reverse_in(self):
         apple = Food.objects.create(name="apple")
         pear = Food.objects.create(name="pear")