diff --git a/src/sssom/io.py b/src/sssom/io.py
index 8f4c947e..d0807e41 100644
--- a/src/sssom/io.py
+++ b/src/sssom/io.py
@@ -130,6 +130,23 @@ def split_file(input_path: str, output_directory: Union[str, Path]) -> None:
     write_tables(splitted, output_directory)
 
 
+def convert_plain_prefix_map_to_extended(prefix_map):
+    """Convert a standard key/val previx map to extended prefix map format"""
+    by_uri_prefix = {}
+    for prefix, uri_prefix in prefix_map.items():
+        if uri_prefix in by_uri_prefix:
+            by_uri_prefix[uri_prefix]["prefix_synonyms"].append(prefix)
+            continue
+        by_uri_prefix[uri_prefix] = {
+            "prefix": prefix,
+            "prefix_synonyms": [],
+            "uri_prefix": uri_prefix,
+            "uri_prefix_synonyms": []
+        }
+    epm = list(by_uri_prefix.values())
+    return epm
+
+
 def get_metadata_and_prefix_map(
     metadata_path: Union[None, str, Path] = None, *, prefix_map_mode: Optional[MergeMode] = None
 ) -> Tuple[Converter, MetadataType]:
@@ -147,7 +164,9 @@ def get_metadata_and_prefix_map(
         metadata = yaml.safe_load(file)
 
     metadata = dict(ChainMap(metadata, get_default_metadata()))
-    converter = Converter.from_prefix_map(metadata.pop(CURIE_MAP, {}))
+    prefix_map = metadata.pop(CURIE_MAP, {})
+    epm = convert_plain_prefix_map_to_extended(prefix_map)
+    converter = Converter.from_extended_prefix_map(epm)
     converter = _merge_converter(converter, prefix_map_mode=prefix_map_mode)
     return converter, metadata
 
diff --git a/src/sssom/util.py b/src/sssom/util.py
index 64db60ed..233f5b2c 100644
--- a/src/sssom/util.py
+++ b/src/sssom/util.py
@@ -234,7 +234,7 @@ def __str__(self) -> str:  # noqa:D105
         description += self.df.tail().to_string() + "\n"
         return description
 
-    def clean_prefix_map(self, strict: bool = True) -> None:
+    def clean_prefix_map(self, strict: bool = True, merge=False) -> None:
         """
         Remove unused prefixes from the internal prefix map based on the internal dataframe.
 
@@ -246,7 +246,11 @@ def clean_prefix_map(self, strict: bool = True) -> None:
         if self.metadata:
             prefixes_in_table.update(get_prefixes_used_in_metadata(self.metadata))
 
-        missing_prefixes = prefixes_in_table - self.converter.get_prefixes()
+        prefixes = {record.prefix for record in self.converter.records}
+        aliases = {p for p in itt.chain(*[record.prefix_synonyms for record in self.converter.records]) if p}
+        converter_prefixes = prefixes | aliases
+        missing_prefixes = prefixes_in_table - converter_prefixes
+
         if missing_prefixes and strict:
             raise ValueError(
                 f"{missing_prefixes} are used in the SSSOM mapping set but it does not exist in the prefix map"
@@ -254,7 +258,7 @@ def clean_prefix_map(self, strict: bool = True) -> None:
 
         subconverter = self.converter.get_subconverter(prefixes_in_table)
         for prefix in missing_prefixes:
-            subconverter.add_prefix(prefix, f"{UNKNOWN_IRI}{prefix.lower()}/")
+            subconverter.add_prefix(prefix, f"{UNKNOWN_IRI}{prefix.lower()}/", merge=merge)
 
         self.converter = subconverter