diff --git a/maubot/__main__.py b/maubot/__main__.py
index a188ff5..586091e 100644
--- a/maubot/__main__.py
+++ b/maubot/__main__.py
@@ -59,8 +59,7 @@ init_zip_loader(config)
 db_session = init_db(config)
 clients = init_client_class(db_session, loop)
 management_api = init_mgmt_api(config, loop)
-server = MaubotServer(config, loop)
-server.app.add_subapp(config["server.base_path"], management_api)
+server = MaubotServer(management_api, config, loop)
 plugins = init_plugin_instance_class(db_session, config, server, loop)
 
 for plugin in plugins:
diff --git a/maubot/plugin_base.py b/maubot/plugin_base.py
index e07cae1..47ae7b4 100644
--- a/maubot/plugin_base.py
+++ b/maubot/plugin_base.py
@@ -24,7 +24,7 @@ from aiohttp import ClientSession
 if TYPE_CHECKING:
     from mautrix.util.config import BaseProxyConfig
     from .client import MaubotMatrixClient
-    from .server import PluginWebApp
+    from .plugin_server import PluginWebApp
 
 
 class Plugin(ABC):
diff --git a/maubot/plugin_server.py b/maubot/plugin_server.py
new file mode 100644
index 0000000..a5dd49a
--- /dev/null
+++ b/maubot/plugin_server.py
@@ -0,0 +1,87 @@
+# maubot - A plugin-based Matrix bot system.
+# Copyright (C) 2018 Tulir Asokan
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+from typing import List, Callable, Awaitable
+from functools import partial
+
+from aiohttp import web, hdrs
+from yarl import URL
+
+Handler = Callable[[web.Request], Awaitable[web.Response]]
+Middleware = Callable[[web.Request, Handler], Awaitable[web.Response]]
+
+
+class PluginWebApp(web.UrlDispatcher):
+    def __init__(self):
+        super().__init__()
+        self._middleware: List[Middleware] = []
+
+    def add_middleware(self, middleware: Middleware) -> None:
+        self._middleware.append(middleware)
+
+    def remove_middleware(self, middleware: Middleware) -> None:
+        self._middleware.remove(middleware)
+
+    def clear(self) -> None:
+        self._resources = []
+        self._named_resources = {}
+        self._middleware = []
+
+    async def handle(self, request: web.Request) -> web.Response:
+        match_info = await self.resolve(request)
+        match_info.freeze()
+        resp = None
+        request._match_info = match_info
+        expect = request.headers.get(hdrs.EXPECT)
+        if expect:
+            resp = await match_info.expect_handler(request)
+            await request.writer.drain()
+        if resp is None:
+            handler = match_info.handler
+            for middleware in self._middleware:
+                handler = partial(middleware, handler=handler)
+            resp = await handler(request)
+        return resp
+
+
+class PrefixResource(web.Resource):
+    def __init__(self, prefix, *, name=None):
+        assert not prefix or prefix.startswith('/'), prefix
+        assert prefix in ('', '/') or not prefix.endswith('/'), prefix
+        super().__init__(name=name)
+        self._prefix = URL.build(path=prefix).raw_path
+
+    @property
+    def canonical(self):
+        return self._prefix
+
+    def get_info(self):
+        return {'path': self._prefix}
+
+    def url_for(self):
+        return URL.build(path=self._prefix, encoded=True)
+
+    def add_prefix(self, prefix):
+        assert prefix.startswith('/')
+        assert not prefix.endswith('/')
+        assert len(prefix) > 1
+        self._prefix = prefix + self._prefix
+
+    def _match(self, path: str) -> dict:
+        return {} if self.raw_match(path) else None
+
+    def raw_match(self, path: str) -> bool:
+        return path and path.startswith(self._prefix)
+
diff --git a/maubot/server.py b/maubot/server.py
index 91e113f..73de847 100644
--- a/maubot/server.py
+++ b/maubot/server.py
@@ -13,18 +13,18 @@
 #
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
-from typing import Tuple, List, Dict, Callable, Awaitable
-from functools import partial
+from typing import Tuple, Dict
 import logging
 import asyncio
 
-from aiohttp import web, hdrs, URL
+from aiohttp import web, hdrs
 from aiohttp.abc import AbstractAccessLogger
 import pkg_resources
 
 from mautrix.api import PathBuilder, Method
 
 from .config import Config
+from .plugin_server import PrefixResource, PluginWebApp
 from .__meta__ import __version__
 
 
@@ -35,78 +35,19 @@ class AccessLogger(AbstractAccessLogger):
                          f'in {round(time, 4)}s"')
 
 
-Handler = Callable[[web.Request], Awaitable[web.Response]]
-Middleware = Callable[[web.Request, Handler], Awaitable[web.Response]]
-
-
-class PluginWebApp(web.UrlDispatcher):
-    def __init__(self):
-        super().__init__()
-        self._middleware: List[Middleware] = []
-
-    def add_middleware(self, middleware: Middleware) -> None:
-        self._middleware.append(middleware)
-
-    def remove_middleware(self, middleware: Middleware) -> None:
-        self._middleware.remove(middleware)
-
-    async def handle(self, request: web.Request) -> web.Response:
-        match_info = await self.resolve(request)
-        match_info.freeze()
-        resp = None
-        request._match_info = match_info
-        expect = request.headers.get(hdrs.EXPECT)
-        if expect:
-            resp = await match_info.expect_handler(request)
-            await request.writer.drain()
-        if resp is None:
-            handler = match_info.handler
-            for middleware in self._middleware:
-                handler = partial(middleware, handler=handler)
-            resp = await handler(request)
-        return resp
-
-
-class PrefixResource(web.Resource):
-    def __init__(self, prefix, *, name=None):
-        assert not prefix or prefix.startswith('/'), prefix
-        assert prefix in ('', '/') or not prefix.endswith('/'), prefix
-        super().__init__(name=name)
-        self._prefix = URL.build(path=prefix).raw_path
-
-    @property
-    def canonical(self):
-        return self._prefix
-
-    def add_prefix(self, prefix):
-        assert prefix.startswith('/')
-        assert not prefix.endswith('/')
-        assert len(prefix) > 1
-        self._prefix = prefix + self._prefix
-
-    def _match(self, path: str) -> dict:
-        return {} if self.raw_match(path) else None
-
-    def raw_match(self, path: str) -> bool:
-        return path and path.startswith(self._prefix)
-
-
 class MaubotServer:
     log: logging.Logger = logging.getLogger("maubot.server")
+    plugin_routes: Dict[str, PluginWebApp]
 
-    def __init__(self, config: Config, loop: asyncio.AbstractEventLoop) -> None:
+    def __init__(self, management_api: web.Application, config: Config,
+                 loop: asyncio.AbstractEventLoop) -> None:
         self.loop = loop or asyncio.get_event_loop()
         self.app = web.Application(loop=self.loop, client_max_size=100 * 1024 * 1024)
         self.config = config
 
-        as_path = PathBuilder(config["server.appservice_base_path"])
-        self.add_route(Method.PUT, as_path.transactions, self.handle_transaction)
-
-        self.plugin_routes: Dict[str, PluginWebApp] = {}
-        resource = PrefixResource(config["server.plugin_base_path"])
-        resource.add_route(hdrs.METH_ANY, self.handle_plugin_path)
-        self.app.router.register_resource(resource)
-
+        self.setup_appservice()
+        self.app.add_subapp(config["server.base_path"], management_api)
+        self.setup_instance_subapps()
         self.setup_management_ui()
 
         self.runner = web.AppRunner(self.app, access_log_class=AccessLogger)
@@ -114,7 +55,8 @@ class MaubotServer:
     async def handle_plugin_path(self, request: web.Request) -> web.Response:
         for path, app in self.plugin_routes.items():
             if request.path.startswith(path):
-                request = request.clone(rel_url=request.path[len(path):])
+                request = request.clone(
+                    rel_url=request.rel_url.with_path(request.rel_url.path[len(path):]))
                 return await app.handle(request)
         return web.Response(status=404)
 
@@ -131,10 +73,20 @@ class MaubotServer:
     def remove_instance_webapp(self, instance_id: str) -> None:
         try:
             subpath = self.config["server.plugin_base_path"] + instance_id
-            self.plugin_routes.pop(subpath)
+            self.plugin_routes.pop(subpath).clear()
         except KeyError:
             return
 
+    def setup_instance_subapps(self) -> None:
+        self.plugin_routes = {}
+        resource = PrefixResource(self.config["server.plugin_base_path"].rstrip("/"))
+        resource.add_route(hdrs.METH_ANY, self.handle_plugin_path)
+        self.app.router.register_resource(resource)
+
+    def setup_appservice(self) -> None:
+        as_path = PathBuilder(self.config["server.appservice_base_path"])
+        self.add_route(Method.PUT, as_path.transactions, self.handle_transaction)
+
     def setup_management_ui(self) -> None:
         ui_base = self.config["server.ui_base_path"]
         if ui_base == "/":