diff --git a/barbican/model/clean.py b/barbican/model/clean.py
index bc95aca01..6e732117d 100644
--- a/barbican/model/clean.py
+++ b/barbican/model/clean.py
@@ -187,7 +187,7 @@ def _soft_delete_expired_secrets(threshold_date):
     """
     current_time = timeutils.utcnow()
     session = repo.get_session()
-    query = session.query(models.Secret.id)
+    query = session.query(models.Secret)
     query = query.filter(~models.Secret.deleted)
     query = query.filter(
         models.Secret.expiration <= threshold_date
diff --git a/barbican/model/migration/alembic_migrations/versions/0f8c192a061f_add_secret_consumers.py b/barbican/model/migration/alembic_migrations/versions/0f8c192a061f_add_secret_consumers.py
index 1a5b7bb2d..8e3fd5a1b 100644
--- a/barbican/model/migration/alembic_migrations/versions/0f8c192a061f_add_secret_consumers.py
+++ b/barbican/model/migration/alembic_migrations/versions/0f8c192a061f_add_secret_consumers.py
@@ -30,10 +30,8 @@ import sqlalchemy as sa
 
 
 def upgrade():
-    ctx = op.get_context()
     con = op.get_bind()
-    table_exists = ctx.dialect.has_table(con.engine,
-                                         "secret_consumer_metadata")
+    table_exists = sa.inspect(con.engine).has_table("secret_consumer_metadata")
     if not table_exists:
         op.create_table(
             "secret_consumer_metadata",
diff --git a/barbican/model/models.py b/barbican/model/models.py
index eda533045..df65be912 100644
--- a/barbican/model/models.py
+++ b/barbican/model/models.py
@@ -353,10 +353,10 @@ class Secret(BASE, SoftDeleteMixIn, ModelBase):
             datum.delete(session)
 
         for secret_ref in self.container_secrets:
-            session.delete(secret_ref)
+            secret_ref.delete(session)
 
         for secret_acl in self.secret_acls:
-            session.delete(secret_acl)
+            secret_acl.delete(session)
 
     def _do_extra_dict_fields(self):
         """Sub-class hook method: return dict of fields."""
diff --git a/barbican/tests/tasks/test_certificate_resources.py b/barbican/tests/tasks/test_certificate_resources.py
index ff8559853..dac76fbf0 100644
--- a/barbican/tests/tasks/test_certificate_resources.py
+++ b/barbican/tests/tasks/test_certificate_resources.py
@@ -664,8 +664,6 @@ class WhenIssuingCertificateRequests(BaseCertificateRequestsTestCase):
                           self.result_follow_on)
 
     def test_should_raise_for_pycrypto_stored_key_no_private_key(self):
-        self.order_meta.update(self.stored_key_meta)
-
         private_key = rsa.generate_private_key(
             public_exponent=65537,
             key_size=2048,
@@ -693,6 +691,11 @@ class WhenIssuingCertificateRequests(BaseCertificateRequestsTestCase):
         secret_repo.delete_entity_by_id(
             self.private_key.id, self.external_project_id)
 
+        # We need to commit deletions or we'll get deleted objects with deleted
+        # set to True.  This is caused by SQLAlchemy's identity mapping and our
+        # use of scoped_session.
+        repositories.commit()
+        self.order.meta.update(self.stored_key_meta)
         self.assertRaises(excep.StoredKeyPrivateKeyNotFound,
                           cert_res.issue_certificate_request,
                           self.order,