diff --git a/dynamic_site/site.py b/dynamic_site/site.py
index 0efaf25..14c85b1 100644
--- a/dynamic_site/site.py
+++ b/dynamic_site/site.py
@@ -12,7 +12,7 @@
     abort,
     request,
     send_from_directory,
-    Blueprint,
+    url_for,
 )
 
 import dynamic_site
@@ -35,7 +35,7 @@ class Site:
     def __init__(
         self,
         apps_path: str,
-        application_root: str = "/",
+        application_root: str = "",
         enforce_dev_mode: bool = False,
         escape_html_in_md: bool = True,
         verbose: bool = False,
@@ -106,13 +106,19 @@ def initialize_flask_server(self) -> None:
             template_folder=f"{self.dynamic_site_path}/templates",
         )
 
-        bp = Blueprint("apps", __name__)
+        def url_for_root(route: str, **kwargs) -> str:
+            url = url_for(route, **kwargs)
+            if self.application_root:
+                url = f"{self.application_root}{url}"
+            return url
 
-        @bp.route("/")
+        self.flask_app.jinja_env.globals.update(url_for_root=url_for_root)
+
+        @self.flask_app.route("/")
         def index():
             return render_template("index.html", title=self.title, text=self.index_text)
 
-        @bp.route("/favicon.ico")
+        @self.flask_app.route("/favicon.ico")
         def favicon():
             return send_from_directory(
                 os.path.join(self.flask_app.root_path, "static"),
@@ -120,14 +126,14 @@ def favicon():
                 mimetype="image/vnd.microsoft.icon",
             )
 
-        @bp.route("/assets/<file>")
+        @self.flask_app.route("/assets/<file>")
         def assets(file):
             return send_from_directory(
                 os.path.join(self.flask_app.root_path, "static", "assets"),
                 file,
             )
 
-        @bp.route("/doc/images/<file>")
+        @self.flask_app.route("/doc/images/<file>")
         def doc(file):
             return send_from_directory(
                 os.path.join(self.flask_app.root_path, "static", "doc", "images"),
@@ -138,8 +144,8 @@ def doc(file):
         # Subdirectory path apps
         # -----------
 
-        @bp.route("/<app_path>")
-        @bp.route("/<path:app_path>")
+        @self.flask_app.route("/<app_path>")
+        @self.flask_app.route("/<path:app_path>")
         def app_path_route(app_path):
             app_name = app_path.replace("/", ".")
             # First check if the app_path corresponds to an index file
@@ -177,7 +183,7 @@ def app_path_route(app_path):
                 "app.html", title=app_title, json_file=json_file, css_file=css_file
             )
 
-        @bp.route("/<path:app_path>/compute", methods=["POST"])
+        @self.flask_app.route("/<path:app_path>/compute", methods=["POST"])
         def app_path_compute(app_path):
             app_name = app_path.replace("/", ".")
             # If the app_name doesn't exist raise a 404
@@ -204,7 +210,7 @@ def app_path_compute(app_path):
             plots = [stage.serialize() for stage in plots]
             return jsonify({"docs": docs, "settings": settings, "plots": plots})
 
-        @bp.route("/<path:app_path>/documentation", methods=["GET"])
+        @self.flask_app.route("/<path:app_path>/documentation", methods=["GET"])
         def app_path_documentation(app_path):
             app_name = app_path.replace("/", ".")
             # If the app_name doesn't exist raise a 404
@@ -218,9 +224,6 @@ def app_path_documentation(app_path):
                 documentation = open(f"{self.apps_path}/{app_path}.md").read()
             return jsonify({"text": documentation})
 
-        self.flask_app.register_blueprint(bp)
-        self.flask_app.config["APPLICATION_ROOT"] = self.application_root
-
     def wsgi(self) -> Flask:
         return self.flask_app
 
diff --git a/dynamic_site/templates/app.html b/dynamic_site/templates/app.html
index 11a5a64..efbd705 100644
--- a/dynamic_site/templates/app.html
+++ b/dynamic_site/templates/app.html
@@ -6,7 +6,7 @@
     <link
       rel="icon"
       type="image/svg+xml"
-      href="{{ url_for('apps.favicon') }}"
+      href="{{ url_for_root('favicon') }}"
     />
     <meta name="description" content="description" />
     <meta name="author" content="author" />
@@ -38,10 +38,10 @@
     <script type="module" src="http://localhost:5173/@vite/client"></script>
     <script type="module" src="http://localhost:5173/src/main.tsx"></script>
     {% else %}
-    <link rel="stylesheet" href="{{ url_for('apps.assets', file=css_file) }}" />
+    <link rel="stylesheet" href="{{ url_for_root('assets', file=css_file) }}" />
     <script
       type="module"
-      src="{{ url_for('apps.assets', file=json_file) }}"
+      src="{{ url_for_root('assets', file=json_file) }}"
     ></script>
     {% endif %}
 
diff --git a/dynamic_site/templates/index.html b/dynamic_site/templates/index.html
index 8025167..11b38c8 100644
--- a/dynamic_site/templates/index.html
+++ b/dynamic_site/templates/index.html
@@ -6,7 +6,7 @@
     <link
       rel="icon"
       type="image/svg+xml"
-      href="{{ url_for('apps.favicon') }}"
+      href="{{ url_for_root('favicon') }}"
     />
     <meta name="description" content="description" />
     <meta name="author" content="author" />
@@ -94,7 +94,7 @@ <h1 class="uk-heading uk-heading-line uk-text-center">
     </div>
     <!-- Home Button -->
     <div style="position: absolute; left: 5px; top: 5px">
-      <a href="{{ url_for('apps.index') }}">
+      <a href="{{ url_for_root('index') }}">
         <span className="ukmargin-small-right" data-uk-icon="home"></span>
       </a>
     </div>