diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index 276ac0b52d5d..8a716b2146ab 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -104,6 +104,7 @@ def __init__(self):
         self.transaction_factory = DefaultWebTransaction
         # Set if trace logging is enabled
         self.trace_logger = None
+        self.session_factories = []
 
     def add_ui_controller(self, controller_name, controller):
         """
@@ -170,10 +171,12 @@ def __call__(self, environ, start_response):
         path_info = environ.get("PATH_INFO", "")
 
         try:
-            self._model.set_request_id(request_id)  # Start SQLAlchemy session scope
+            for session_factory in self.session_factories:
+                session_factory.set_request_id(request_id)  # Start SQLAlchemy session scope
             return self.handle_request(request_id, path_info, environ, start_response)
         finally:
-            self._model.unset_request_id(request_id)  # End SQLAlchemy session scope
+            for session_factory in self.session_factories:
+                session_factory.unset_request_id(request_id)  # End SQLAlchemy session scope
             self.trace(message="Handle request finished")
             if self.trace_logger:
                 self.trace_logger.context_remove("request_id")
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index b07a424e06f3..6ba4b4745a34 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -120,7 +120,7 @@ def __init__(
 
         # We need this to set the REQUEST_ID contextvar in model.base *BEFORE* a GalaxyWebTransaction is created.
         # This will ensure a SQLAlchemy session is request-scoped for legacy (non-fastapi) endpoints.
-        self._model = galaxy_app.model
+        self.session_factories.append(galaxy_app.model)
 
     def build_apispec(self):
         """
diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index 66e12cc4fd9b..5d3d82f43549 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -98,10 +98,12 @@ async def get_app_with_request_session() -> AsyncGenerator[StructuredApp, None]:
     app = get_app()
     request_id = request_context.data["X-Request-ID"]
     app.model.set_request_id(request_id)
+    app.install_model.set_request_id(request_id)
     try:
         yield app
     finally:
         app.model.unset_request_id(request_id)
+        app.install_model.unset_request_id(request_id)
 
 
 DependsOnApp = cast(StructuredApp, Depends(get_app_with_request_session))
@@ -118,9 +120,10 @@ def __init__(self, callable, dep_type):
         self.galaxy_type_depends = dep_type
 
 
-def depends(dep_type: Type[T], get_app=get_app) -> T:
-    def _do_resolve(request: Request):
-        return get_app().resolve(dep_type)
+def depends(dep_type: Type[T], app=get_app_with_request_session) -> T:
+    async def _do_resolve(request: Request):
+        async for _dep in app():
+            yield _dep.resolve(dep_type)
 
     return cast(T, GalaxyTypeDepends(_do_resolve, dep_type))
 
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 47e8d47ca971..054f67441289 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -7,6 +7,7 @@
 import sys
 import threading
 import traceback
+from typing import Optional
 from urllib.parse import urljoin
 
 from paste import httpexceptions
@@ -20,6 +21,7 @@
 import galaxy.webapps.base.webapp
 from galaxy import util
 from galaxy.security.validate_user_input import VALID_PUBLICNAME_RE
+from galaxy.structured_app import MinimalApp
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties
 from galaxy.web.framework.middleware.error import ErrorMiddleware
@@ -34,6 +36,12 @@
 class GalaxyWebApplication(galaxy.webapps.base.webapp.WebApplication):
     injection_aware = True
 
+    def __init__(
+        self, galaxy_app: MinimalApp, session_cookie: str = "galaxysession", name: Optional[str] = None
+    ) -> None:
+        super().__init__(galaxy_app, session_cookie, name)
+        self.session_factories.append(galaxy_app.install_model)
+
 
 def app_factory(*args, **kwargs):
     """
diff --git a/lib/tool_shed/webapp/api2/__init__.py b/lib/tool_shed/webapp/api2/__init__.py
index 845e1a9a2cfc..52da82a00207 100644
--- a/lib/tool_shed/webapp/api2/__init__.py
+++ b/lib/tool_shed/webapp/api2/__init__.py
@@ -81,7 +81,7 @@ async def get_app_with_request_session() -> AsyncGenerator[ToolShedApp, None]:
 
 
 def depends(dep_type: Type[T]) -> T:
-    return framework_depends(dep_type, get_app=get_app)
+    return framework_depends(dep_type, app=get_app_with_request_session)
 
 
 def get_api_user(