diff --git a/pillar/api/activities.py b/pillar/api/activities.py
index 107377e3..d81bafb6 100644
--- a/pillar/api/activities.py
+++ b/pillar/api/activities.py
@@ -91,14 +91,14 @@ def notification_parse(notification):
 
 
 def notification_get_subscriptions(context_object_type, context_object_id, actor_user_id):
-    subscriptions_collection = current_app.data.driver.db['activities-subscriptions']
+    subscriptions_collection = current_app.db('activities-subscriptions')
     lookup = {
         'user': {"$ne": actor_user_id},
         'context_object_type': context_object_type,
         'context_object': context_object_id,
         'is_subscribed': True,
     }
-    return subscriptions_collection.find(lookup)
+    return subscriptions_collection.find(lookup), subscriptions_collection.count_documents(lookup)
 
 
 def activity_subscribe(user_id, context_object_type, context_object_id):
@@ -140,10 +140,10 @@ def activity_object_add(actor_user_id, verb, object_type, object_id,
     :param object_id: object id, to be traced with object_type_id
     """
 
-    subscriptions = notification_get_subscriptions(
+    subscriptions, subscription_count = notification_get_subscriptions(
         context_object_type, context_object_id, actor_user_id)
 
-    if subscriptions.count() == 0:
+    if subscription_count == 0:
         return
 
     info, status = register_activity(actor_user_id, verb, object_type, object_id,
diff --git a/pillar/api/blender_cloud/home_project.py b/pillar/api/blender_cloud/home_project.py
index 90d005ce..b5ce6933 100644
--- a/pillar/api/blender_cloud/home_project.py
+++ b/pillar/api/blender_cloud/home_project.py
@@ -257,7 +257,7 @@ def has_home_project(user_id):
     """Returns True iff the user has a home project."""
 
     proj_coll = current_app.data.driver.db['projects']
-    return proj_coll.count({'user': user_id, 'category': 'home', '_deleted': False}) > 0
+    return proj_coll.count_documents({'user': user_id, 'category': 'home', '_deleted': False}) > 0
 
 
 def get_home_project(user_id, projection=None):
@@ -272,10 +272,10 @@ def is_home_project(project_id, user_id):
     """Returns True iff the given project exists and is the user's home project."""
 
     proj_coll = current_app.data.driver.db['projects']
-    return proj_coll.count({'_id': project_id,
-                            'user': user_id,
-                            'category': 'home',
-                            '_deleted': False}) > 0
+    return proj_coll.count_documents({'_id': project_id,
+                                      'user': user_id,
+                                      'category': 'home',
+                                      '_deleted': False}) > 0
 
 
 def mark_node_updated(node_id):
diff --git a/pillar/api/file_storage/__init__.py b/pillar/api/file_storage/__init__.py
index 4eda6d3f..1d2b2840 100644
--- a/pillar/api/file_storage/__init__.py
+++ b/pillar/api/file_storage/__init__.py
@@ -566,12 +566,9 @@ def on_pre_get_files(_, lookup):
     lookup_expired['link_expires'] = {'$lte': now}
 
     cursor = current_app.data.find('files', parsed_req, lookup_expired)
-    if cursor.count() == 0:
-        return
-
-    log.debug('Updating expired links for %d files that matched lookup %s',
-              cursor.count(), lookup_expired)
-    for file_doc in cursor:
+    for idx, file_doc in enumerate(cursor):
+        if idx == 0:
+            log.debug('Updating expired links for files that matched lookup %s', lookup_expired)
         # log.debug('Updating expired links for file %r.', file_doc['_id'])
         generate_all_links(file_doc, now)
 
@@ -595,15 +592,14 @@ def refresh_links_for_project(project_uuid, chunk_size, expiry_seconds):
          'link_expires': {'$lt': expire_before},
          }).sort([('link_expires', pymongo.ASCENDING)]).limit(chunk_size)
 
-    if to_refresh.count() == 0:
-        log.info('No links to refresh.')
-        return
-
+    refresh_count = 0
     for file_doc in to_refresh:
         log.debug('Refreshing links for file %s', file_doc['_id'])
         generate_all_links(file_doc, now)
+        refresh_count += 1
 
-    log.info('Refreshed %i links', min(chunk_size, to_refresh.count()))
+    if refresh_count:
+        log.info('Refreshed %i links', refresh_count)
 
 
 def refresh_links_for_backend(backend_name, chunk_size, expiry_seconds):
@@ -621,14 +617,13 @@ def refresh_links_for_backend(backend_name, chunk_size, expiry_seconds):
     my_log.info('Limiting to links that expire before %s', expire_before)
 
     base_query = {'backend': backend_name, '_deleted': {'$ne': True}}
-    to_refresh = files_collection.find(
-        {'$or': [{'link_expires': None, **base_query},
-                 {'link_expires': {'$lt': expire_before}, **base_query},
-                 {'link': None, **base_query}]
-         }).sort([('link_expires', pymongo.ASCENDING)]).limit(
-        chunk_size).batch_size(5)
+    to_refresh_query = {
+        '$or': [{'link_expires': None, **base_query},
+                {'link_expires': {'$lt': expire_before}, **base_query},
+                {'link': None, **base_query}]
+    }
 
-    document_count = to_refresh.count()
+    document_count = files_collection.count_documents(to_refresh_query)
     if document_count == 0:
         my_log.info('No links to refresh.')
         return
@@ -639,6 +634,11 @@ def refresh_links_for_backend(backend_name, chunk_size, expiry_seconds):
     else:
         my_log.info('Found %d documents to refresh, chunk size=%d', document_count, chunk_size)
 
+    to_refresh = files_collection.find(to_refresh_query)\
+            .sort([('link_expires', pymongo.ASCENDING)])\
+            .limit(chunk_size)\
+            .batch_size(5)
+
     refreshed = 0
     report_chunks = min(max(5, document_count // 25), 100)
     for file_doc in to_refresh:
@@ -649,7 +649,7 @@ def refresh_links_for_backend(backend_name, chunk_size, expiry_seconds):
                 my_log.debug('Skipping file %s, it has no project.', file_id)
                 continue
 
-            count = proj_coll.count({'_id': project_id, '$or': [
+            count = proj_coll.count_documents({'_id': project_id, '$or': [
                 {'_deleted': {'$exists': False}},
                 {'_deleted': False},
             ]})
diff --git a/pillar/api/organizations/__init__.py b/pillar/api/organizations/__init__.py
index 6ab7059a..f6903f8e 100644
--- a/pillar/api/organizations/__init__.py
+++ b/pillar/api/organizations/__init__.py
@@ -153,7 +153,7 @@ class OrgManager:
         org_coll = current_app.db('organizations')
         users_coll = current_app.db('users')
 
-        if users_coll.count({'_id': user_id}) == 0:
+        if users_coll.count_documents({'_id': user_id}) == 0:
             raise ValueError('User not found')
 
         self._log.info('Updating organization %s, setting admin user to %s', org_id, user_id)
@@ -189,7 +189,7 @@ class OrgManager:
             if user_doc is not None:
                 user_id = user_doc['_id']
 
-        if user_id and not users_coll.count({'_id': user_id}):
+        if user_id and not users_coll.count_documents({'_id': user_id}):
             raise wz_exceptions.UnprocessableEntity('User does not exist')
 
         self._log.info('Removing user %s / %s from organization %s', user_id, email, org_id)
@@ -385,7 +385,7 @@ class OrgManager:
 
         org_coll = current_app.db('organizations')
 
-        org_count = org_coll.count({'$or': [
+        org_count = org_coll.count_documents({'$or': [
             {'admin_uid': user_id},
             {'members': user_id}
         ]})
@@ -396,7 +396,7 @@ class OrgManager:
         """Return True iff the email is an unknown member of some org."""
 
         org_coll = current_app.db('organizations')
-        org_count = org_coll.count({'unknown_members': member_email})
+        org_count = org_coll.count_documents({'unknown_members': member_email})
         return bool(org_count)
 
     def roles_for_ip_address(self, remote_addr: str) -> typing.Set[str]:
diff --git a/pillar/api/projects/merging.py b/pillar/api/projects/merging.py
index 46e37b37..8736e02d 100644
--- a/pillar/api/projects/merging.py
+++ b/pillar/api/projects/merging.py
@@ -25,8 +25,11 @@ def merge_project(pid_from: ObjectId, pid_to: ObjectId):
 
     # Move the files first. Since this requires API calls to an external
     # service, this is more likely to go wrong than moving the nodes.
-    to_move = files_coll.find({'project': pid_from}, projection={'_id': 1})
-    log.info('Moving %d files to project %s', to_move.count(), pid_to)
+    query = {'project': pid_from}
+    to_move = files_coll.find(query, projection={'_id': 1})
+
+    to_move_count = files_coll.count_documents(query)
+    log.info('Moving %d files to project %s', to_move_count, pid_to)
     for file_doc in to_move:
         fid = file_doc['_id']
         log.debug('moving file %s to project %s', fid, pid_to)
@@ -35,7 +38,7 @@ def merge_project(pid_from: ObjectId, pid_to: ObjectId):
     # Mass-move the nodes.
     etag = random_etag()
     result = nodes_coll.update_many(
-        {'project': pid_from},
+        query,
         {'$set': {'project': pid_to,
                   '_etag': etag,
                   '_updated': utcnow(),
diff --git a/pillar/api/projects/routes.py b/pillar/api/projects/routes.py
index 321d6e80..670cd85a 100644
--- a/pillar/api/projects/routes.py
+++ b/pillar/api/projects/routes.py
@@ -92,8 +92,8 @@ def project_manage_users():
                     action, current_user_id)
         raise wz_exceptions.UnprocessableEntity()
 
-    users_collection.update({'_id': target_user_id},
-                            {operation: {'groups': admin_group['_id']}})
+    users_collection.update_one({'_id': target_user_id},
+                                {operation: {'groups': admin_group['_id']}})
 
     user = users_collection.find_one({'_id': target_user_id},
                                      {'username': 1, 'email': 1,
@@ -141,5 +141,3 @@ def get_allowed_methods(project_id=None, node_type=None):
     resp.status_code = 204
 
     return resp
-
-
diff --git a/pillar/api/timeline.py b/pillar/api/timeline.py
index 5731ff39..b2922d73 100644
--- a/pillar/api/timeline.py
+++ b/pillar/api/timeline.py
@@ -91,7 +91,7 @@ class SearchHelper:
 
     def has_more(self, continue_from: datetime) -> bool:
         nodes_coll = current_app.db('nodes')
-        result = nodes_coll.count(self._match(continue_from))
+        result = nodes_coll.count_documents(self._match(continue_from))
         return bool(result)
 
 
diff --git a/pillar/cli/maintenance.py b/pillar/cli/maintenance.py
index 8dc873ae..30880d35 100644
--- a/pillar/cli/maintenance.py
+++ b/pillar/cli/maintenance.py
@@ -306,7 +306,7 @@ def purge_home_projects(go=False):
                 yield pid
                 continue
 
-            if users_coll.find({'_id': uid, '_deleted': {'$ne': True}}).count() == 0:
+            if users_coll.count_documents({'_id': uid, '_deleted': {'$ne': True}}) == 0:
                 log.info('Project %s has non-existing owner %s', pid, uid)
                 bad += 1
                 yield pid
@@ -1296,9 +1296,9 @@ def fix_missing_activities_subscription_defaults(user=None, context_object=None,
         lookup_is_subscribed['context_object'] = ObjectId(context_object)
         lookup_notifications['context_object'] = ObjectId(context_object)
 
-    num_need_is_subscribed_update = subscriptions_collection.count(lookup_is_subscribed)
+    num_need_is_subscribed_update = subscriptions_collection.count_documents(lookup_is_subscribed)
     log.info("Found %d documents that needs to be update 'is_subscribed'", num_need_is_subscribed_update)
-    num_need_notification_web_update = subscriptions_collection.count(lookup_notifications)
+    num_need_notification_web_update = subscriptions_collection.count_documents(lookup_notifications)
     log.info("Found %d documents that needs to be update 'notifications.web'", num_need_notification_web_update)
 
     if not go:
@@ -1306,29 +1306,27 @@ def fix_missing_activities_subscription_defaults(user=None, context_object=None,
 
     if num_need_is_subscribed_update > 0:
         log.info("Updating 'is_subscribed'")
-        resp = subscriptions_collection.update(
+        resp = subscriptions_collection.update_many(
             lookup_is_subscribed,
             {
                 '$set': {'is_subscribed': True}
             },
-            multi=True,
             upsert=False
         )
-        if resp['nModified'] is not num_need_is_subscribed_update:
+        if resp.modified_count != num_need_is_subscribed_update:
             log.warning("Expected % documents to be update, was %d",
                         num_need_is_subscribed_update, resp['nModified'])
 
     if num_need_notification_web_update > 0:
         log.info("Updating 'notifications.web'")
-        resp = subscriptions_collection.update(
+        resp = subscriptions_collection.update_many(
             lookup_notifications,
             {
                 '$set': {'notifications.web': True}
             },
-            multi=True,
             upsert=False
         )
-        if resp['nModified'] is not num_need_notification_web_update:
+        if resp.modified_count != num_need_notification_web_update:
             log.warning("Expected % documents to be update, was %d",
                         num_need_notification_web_update, resp['nModified'])
 
diff --git a/pillar/cli/operations.py b/pillar/cli/operations.py
index 0d0216e0..c1f3df3f 100644
--- a/pillar/cli/operations.py
+++ b/pillar/cli/operations.py
@@ -165,49 +165,6 @@ def merge_project(src_proj_url, dest_proj_url):
     log.info('Done moving.')
 
 
-@manager_operations.command
-def index_users_rebuild():
-    """Clear users index, update settings and reindex all users."""
-
-    import concurrent.futures
-
-    from pillar.api.utils.algolia import algolia_index_user_save
-
-    users_index = current_app.algolia_index_users
-    if users_index is None:
-        log.error('Algolia is not configured properly, unable to do anything!')
-        return 1
-
-    log.info('Dropping existing index: %s', users_index)
-    users_index.clear_index()
-    index_users_update_settings()
-
-    db = current_app.db()
-    users = db['users'].find({'_deleted': {'$ne': True}})
-    user_count = users.count()
-
-    log.info('Reindexing all %i users', user_count)
-
-    real_current_app = current_app._get_current_object()._get_current_object()
-
-    def do_user(user):
-        with real_current_app.app_context():
-            algolia_index_user_save(user)
-
-    with concurrent.futures.ThreadPoolExecutor(max_workers=10) as executor:
-        future_to_user = {executor.submit(do_user, user): user
-                          for user in users}
-        for idx, future in enumerate(concurrent.futures.as_completed(future_to_user)):
-            user = future_to_user[future]
-            user_ident = user.get('email') or user.get('_id')
-            try:
-                future.result()
-            except Exception:
-                log.exception('Error updating user %i/%i %s', idx + 1, user_count, user_ident)
-            else:
-                log.info('Updated user %i/%i %s', idx + 1, user_count, user_ident)
-
-
 @manager_operations.command
 def index_users_update_settings():
     """Configure indexing backend as required by the project"""
@@ -234,7 +191,7 @@ def hash_auth_tokens():
     tokens_coll = current_app.db('tokens')
     query = {'token': {'$exists': True}}
     cursor = tokens_coll.find(query, projection={'token': 1, '_id': 1})
-    log.info('Updating %d tokens', cursor.count())
+    log.info('Updating %d tokens', tokens_coll.count_documents(query))
 
     for token_doc in cursor:
         hashed_token = hash_auth_token(token_doc['token'])
diff --git a/tests/test_api/test_auth.py b/tests/test_api/test_auth.py
index 349da074..b19fda5b 100644
--- a/tests/test_api/test_auth.py
+++ b/tests/test_api/test_auth.py
@@ -741,7 +741,7 @@ class UserCreationTest(AbstractPillarTest):
 
         with self.app.test_request_context():
             users_coll = self.app.db().users
-            self.assertEqual(0, users_coll.count())
+            self.assertEqual(0, users_coll.count_documents({}))
 
         self.mock_blenderid_validate_happy()
         token = 'this is my life now'
@@ -749,7 +749,7 @@ class UserCreationTest(AbstractPillarTest):
 
         with self.app.test_request_context():
             users_coll = self.app.db().users
-            self.assertEqual(1, users_coll.count())
+            self.assertEqual(1, users_coll.count_documents({}))
 
             db_user = users_coll.find()[0]
             self.assertEqual(db_user['email'], TEST_EMAIL_ADDRESS)
@@ -760,7 +760,7 @@ class UserCreationTest(AbstractPillarTest):
 
         with self.app.test_request_context():
             users_coll = self.app.db().users
-            self.assertEqual(0, users_coll.count())
+            self.assertEqual(0, users_coll.count_documents({}))
 
         bid_resp = {'status': 'success',
                     'user': {'email': TEST_EMAIL_ADDRESS,
@@ -778,7 +778,7 @@ class UserCreationTest(AbstractPillarTest):
 
         with self.app.test_request_context():
             users_coll = self.app.db().users
-            self.assertEqual(1, users_coll.count())
+            self.assertEqual(1, users_coll.count_documents({}))
 
             db_user = users_coll.find()[0]
             self.assertEqual(db_user['email'], TEST_EMAIL_ADDRESS)
@@ -789,7 +789,7 @@ class UserCreationTest(AbstractPillarTest):
         """Blender ID does not require full name, we do."""
         with self.app.app_context():
             users_coll = self.app.db().users
-            self.assertEqual(0, users_coll.count())
+            self.assertEqual(0, users_coll.count_documents({}))
 
         # First request will create the user, the 2nd request will update.
         self.mock_blenderid_validate_happy()
@@ -818,7 +818,7 @@ class UserCreationTest(AbstractPillarTest):
         self.get('/api/users/me', auth_token=token)
 
         with self.app.app_context():
-            self.assertEqual(1, users_coll.count())
+            self.assertEqual(1, users_coll.count_documents({}))
 
             db_user = users_coll.find()[0]
             self.assertEqual(db_user['email'], TEST_EMAIL_ADDRESS)
diff --git a/tests/test_api/test_comments.py b/tests/test_api/test_comments.py
index 4679c5e1..21586bf9 100644
--- a/tests/test_api/test_comments.py
+++ b/tests/test_api/test_comments.py
@@ -81,7 +81,7 @@ class CommentEditTest(AbstractPillarTest):
 
         with self.app.app_context():
             proj_coll = self.app.db('projects')
-            proj_coll.update(
+            proj_coll.update_one(
                 {'_id': self.pid},
                 {'$set': {
                     'node_types': self.project['node_types'],
diff --git a/tests/test_api/test_nodes.py b/tests/test_api/test_nodes.py
index 4fb59695..497f52b7 100644
--- a/tests/test_api/test_nodes.py
+++ b/tests/test_api/test_nodes.py
@@ -690,7 +690,7 @@ class NodesReferencedByProjectTest(AbstractPillarTest):
         self.node_etag = node['_etag']
 
         with self.app.app_context():
-            self.app.db('projects').update(
+            self.app.db('projects').update_one(
                 {'_id': self.pid},
                 {'$set': {
                     'header_node': self.node_id,
diff --git a/tests/test_api/test_organizations.py b/tests/test_api/test_organizations.py
index 4a4120fe..7497c678 100644
--- a/tests/test_api/test_organizations.py
+++ b/tests/test_api/test_organizations.py
@@ -24,13 +24,13 @@ class OrganizationCruTest(AbstractPillarTest):
         self.enter_app_context()
 
         # There should be no organizations to begin with.
-        db = self.app.db('organizations')
-        self.assertEqual(0, db.count())
+        org_coll = self.app.db('organizations')
+        self.assertEqual(0, org_coll.count_documents({}))
 
         admin_uid = self.create_user(24 * 'a')
         org_doc = self.app.org_manager.create_new_org('Хакеры', admin_uid, 25)
 
-        self.assertIsNotNone(db.find_one(org_doc['_id']))
+        self.assertIsNotNone(org_coll.find_one(org_doc['_id']))
         self.assertEqual(bson.ObjectId(24 * 'a'), org_doc['admin_uid'])
         self.assertEqual('Хакеры', org_doc['name'])
         self.assertEqual(25, org_doc['seat_count'])