diff --git a/rhodecode/lib/audit_logger.py b/rhodecode/lib/audit_logger.py
--- a/rhodecode/lib/audit_logger.py
+++ b/rhodecode/lib/audit_logger.py
@@ -261,7 +261,6 @@ def store(action, user, action_data=None
         ip_address = safe_unicode(ip_addr)
 
         with sa_session.no_autoflush:
-            update_user_last_activity(sa_session, user_id)
 
             user_log = _store_log(
                 action_name=action_name,
@@ -275,11 +274,15 @@ def store(action, user, action_data=None
             )
 
             sa_session.add(user_log)
+            if commit:
+                sa_session.commit()
+            entry_id = user_log.entry_id or ''
+
+            update_user_last_activity(sa_session, user_id)
 
             if commit:
                 sa_session.commit()
 
-        entry_id = user_log.entry_id or ''
         log.info('AUDIT[%s]: Logging action: `%s` by user:id:%s[%s] ip:%s',
                  entry_id, action_name, user_id, username, ip_address)
 
@@ -295,4 +298,6 @@ def update_user_last_activity(sa_session
         log.debug(
             'updated user `%s` last activity to:%s', user_id, _last_activity)
     except Exception:
-        log.exception("Failed last activity update")
+        log.exception("Failed last activity update for user_id: %s", user_id)
+        sa_session.rollback()
+
diff --git a/rhodecode/model/pull_request.py b/rhodecode/model/pull_request.py
--- a/rhodecode/model/pull_request.py
+++ b/rhodecode/model/pull_request.py
@@ -1198,14 +1198,20 @@ class PullRequestModel(BaseModel):
                     pull_request=pull_request,
                     revision=commit_id)
 
+        # initial commit
+        Session().commit()
+
+        if pr_has_changes:
             # send update email to users
             try:
                 self.notify_users(pull_request=pull_request, updating_user=updating_user,
                                   ancestor_commit_id=ancestor_commit_id,
                                   commit_changes=commit_changes,
                                   file_changes=file_changes)
+                Session().commit()
             except Exception:
                 log.exception('Failed to send email notification to users')
+                Session().rollback()
 
         log.debug(
             'Updated pull request %s, added_ids: %s, common_ids: %s, '
@@ -1221,7 +1227,7 @@ class PullRequestModel(BaseModel):
             pull_request.pull_request_id, source_ref_id,
             pull_request.source_ref_parts.commit_id,
             pull_request_version.pull_request_version_id)
-        Session().commit()
+
         self.trigger_pull_request_hook(pull_request, pull_request.author, 'update')
 
         return UpdateResponse(