diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 0d53703b0550..ec902bc59fce 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -12,7 +12,6 @@
 from markupsafe import escape
 from sqlalchemy import (
     and_,
-    desc,
     exc,
     func,
     true,
@@ -26,7 +25,6 @@
     util,
 )
 from galaxy.managers import (
-    api_keys,
     base,
     deletable,
 )
@@ -66,7 +64,6 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
     #   most of which it may be unneccessary to have here
 
     # TODO: incorp BaseAPIController.validate_in_users_and_groups
-    # TODO: incorp CreatesApiKeysMixin
     # TODO: incorporate UsesFormDefinitionsMixin?
     def __init__(self, app: BasicSharedApp):
         self.model_class = app.model.User
@@ -358,15 +355,6 @@ def current_user(self, trans):
         # TODO: trans
         return trans.user
 
-    # ---- api keys
-    def create_api_key(self, user: model.User) -> model.APIKeys:
-        """
-        Create and return an API key for `user`.
-        """
-        # TODO: seems like this should return the model
-        # Also TODO: seems unused? drop and see what happens? -John
-        return api_keys.ApiKeyManager(self.app).create_api_key(user)
-
     def user_can_do_run_as(self, user) -> bool:
         run_as_users = [u for u in self.app.config.get("api_allow_run_as", "").split(",") if u]
         if not run_as_users:
@@ -376,28 +364,6 @@ def user_can_do_run_as(self, user) -> bool:
         can_do_run_as = user_in_run_as_users or user.bootstrap_admin_user
         return can_do_run_as
 
-    # TODO: possibly move to ApiKeyManager
-    def valid_api_key(self, user):
-        """
-        Return this most recent APIKey for this user or None if none have been created.
-        """
-        query = self.session().query(model.APIKeys).filter_by(user=user).order_by(desc(model.APIKeys.create_time))
-        all = query.all()
-        if len(all):
-            return all[0]
-        return None
-
-    # TODO: possibly move to ApiKeyManager
-    def get_or_create_valid_api_key(self, user):
-        """
-        Return this most recent APIKey for this user or create one if none have been
-        created.
-        """
-        existing = self.valid_api_key(user)
-        if existing:
-            return existing
-        return self.create_api_key(self, user)
-
     # ---- preferences
     def preferences(self, user):
         return {key: value for key, value in user.preferences.items()}
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index 8ddd2ef49e94..e581491bf002 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -24,7 +24,6 @@
 )
 from galaxy.datatypes.interval import ChromatinInteractions
 from galaxy.managers import (
-    api_keys,
     base as managers_base,
     configuration,
     users,
@@ -382,17 +381,6 @@ def __init__(self, extension, dtype, type_extension, mimetype, display_in_upload
 #
 
 
-class CreatesApiKeysMixin:
-    """
-    Mixing centralizing logic for creating API keys for user objects.
-
-    Deprecated - please use api_keys.ApiKeyManager for new development.
-    """
-
-    def create_api_key(self, trans, user: model.User) -> model.APIKeys:
-        return api_keys.ApiKeyManager(trans.app).create_api_key(user)
-
-
 class SharableItemSecurityMixin:
     """Mixin for handling security for sharable items."""
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 59d72c209804..985fdc60badd 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -29,7 +29,6 @@
 )
 from galaxy.webapps.base.controller import (
     BaseUIController,
-    CreatesApiKeysMixin,
     UsesFormDefinitionsMixin,
 )
 from ..api import depends
@@ -41,7 +40,7 @@ def _filtered_registration_params_dict(payload):
     return {k: v for (k, v) in payload.items() if k in ["email", "username", "password", "confirm", "subscribe"]}
 
 
-class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
+class User(BaseUIController, UsesFormDefinitionsMixin):
     user_manager: users.UserManager = depends(users.UserManager)
     installed_len_files = None
 
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index 45649b05fb69..1d8a4ba7fb87 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -8,6 +8,7 @@
     util,
     web,
 )
+from galaxy.managers.api_keys import ApiKeyManager
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
@@ -313,7 +314,7 @@ def api_keys(self, trans, cntrller, **kwd):
         message = escape(util.restore_text(params.get("message", "")))
         status = params.get("status", "done")
         if params.get("new_api_key_button", False):
-            self.create_api_key(trans, trans.user)
+            ApiKeyManager(trans.app).create_api_key(trans.user)
             message = "Generated a new web API key"
             status = "done"
         return trans.fill_template(