diff --git a/src/olmo_core/config.py b/src/olmo_core/config.py
index d6ef4f12..a211b729 100644
--- a/src/olmo_core/config.py
+++ b/src/olmo_core/config.py
@@ -170,7 +170,9 @@ def merge(self, dotlist: List[str], prefix: Optional[str] = None, strict: bool =
         try:
             dotlist = _clean_opts(dotlist)
             if prefix is not None:
-                dotlist = [o.lstrip(f"{prefix}.") for o in dotlist if o.startswith(f"{prefix}.")]
+                dotlist = [
+                    o.replace(f"{prefix}.", "", 1) for o in dotlist if o.startswith(f"{prefix}.")
+                ]
             if not strict:
                 field_names = set(f.name for f in fields(self))
                 dotlist = [