diff --git a/lib/esbonio/esbonio/sphinx_agent/config.py b/lib/esbonio/esbonio/sphinx_agent/config.py
index 1bb6de22..e491dcd4 100644
--- a/lib/esbonio/esbonio/sphinx_agent/config.py
+++ b/lib/esbonio/esbonio/sphinx_agent/config.py
@@ -160,7 +160,9 @@ def to_application_args(self, context: dict[str, Any]) -> dict[str, Any]:
                 continue
 
             replacement = self.resolve_config_variable(match.group(1), context)
-            setattr(self, name, VARIABLE.sub(replacement, value))
+            result = VARIABLE.sub(re.escape(replacement), value)
+
+            setattr(self, name, result)
 
         build_dir = pathlib.Path(self.build_dir).resolve()
         doctree_dir = pathlib.Path(self.doctree_dir).resolve()