diff --git a/python/CHANGELOG.rst b/python/CHANGELOG.rst
index 7f4027dbf8..18907ba2e5 100644
--- a/python/CHANGELOG.rst
+++ b/python/CHANGELOG.rst
@@ -1,3 +1,12 @@
+--------------------
+[0.6.2] - 2025-XX-XX
+--------------------
+
+**Bugfixes**
+
+- Meatdata.schema was returning a modified schema, this is fixed to return a copy of
+  the original schema instead (:user:`benjeffery`, :issue:`3129`, :pr:`3130`)
+
 --------------------
 [0.6.1] - 2025-03-31
 --------------------
diff --git a/python/tests/test_metadata.py b/python/tests/test_metadata.py
index 632604deba..ce999e3fc3 100644
--- a/python/tests/test_metadata.py
+++ b/python/tests/test_metadata.py
@@ -1125,6 +1125,25 @@ def test_defaults_object_or_null(self):
         assert ms.validate_and_encode_row(None) == b""
         assert ms.decode_row(b"") is None
 
+    def test_add_property_to_schema(self):
+        schema = metadata.MetadataSchema(
+            {
+                "codec": "struct",
+                "type": ["object", "null"],
+                "name": "Mutation metadata",
+                "properties": {
+                    "s": {"type": "number", "binaryFormat": "d"},
+                },
+                "additionalProperties": False,
+            }
+        )
+        schema_with_additional = schema.schema
+        schema_with_additional["properties"]["a"] = {
+            "type": "number",
+            "binaryFormat": "d",
+        }
+        metadata.MetadataSchema(schema_with_additional)
+
 
 class TestStructCodecRoundTrip:
     def round_trip(self, schema, row_data):
diff --git a/python/tskit/_version.py b/python/tskit/_version.py
index 4d546301e4..10ab1b2014 100644
--- a/python/tskit/_version.py
+++ b/python/tskit/_version.py
@@ -1,4 +1,4 @@
 # Definitive location for the version number.
 # During development, should be x.y.z.devN
 # For beta should be x.y.zbN
-tskit_version = "0.6.1"
+tskit_version = "0.6.2.dev0"
diff --git a/python/tskit/metadata.py b/python/tskit/metadata.py
index 7c217b553e..d40c3df262 100644
--- a/python/tskit/metadata.py
+++ b/python/tskit/metadata.py
@@ -778,6 +778,7 @@ class MetadataSchema:
 
     def __init__(self, schema: Mapping[str, Any] | None) -> None:
         self._schema = schema
+        self._unmodified_schema = schema
         self._bypass_validation = False
 
         if schema is None:
@@ -835,7 +836,7 @@ def __eq__(self, other) -> bool:
     @property
     def schema(self) -> Mapping[str, Any] | None:
         # Return a copy to avoid unintentional mutation
-        return copy.deepcopy(self._schema)
+        return copy.deepcopy(self._unmodified_schema)
 
     def asdict(self) -> Mapping[str, Any] | None:
         """