diff --git a/preprocess_schemas.py b/preprocess_schemas.py
index a4fe2e9..9d433ab 100644
--- a/preprocess_schemas.py
+++ b/preprocess_schemas.py
@@ -104,6 +104,10 @@ def _process_all_of_item(item, node, root, state):
     if not isinstance(item, dict):
         return
 
+    if any(key in item for key in ("if", "then", "else")):
+        state["remaining_refs"].append(item)
+        return
+
     # Extract polymorphic branches (anyOf, oneOf) to keep the node flat
     for poly_key in ["anyOf", "oneOf"]:
         if poly_key in item:
diff --git a/tests/test_codegen_pipeline.py b/tests/test_codegen_pipeline.py
index fe4d863..8519a41 100644
--- a/tests/test_codegen_pipeline.py
+++ b/tests/test_codegen_pipeline.py
@@ -91,6 +91,29 @@ def test_preprocess_flattens_and_distributes_properties(self) -> None:
         self.assertEqual(set(branch["required"]), {"id", "kind"})
         self.assertEqual(branch["type"], "object")
 
+    def test_preprocess_preserves_multiple_conditional_branches(self) -> None:
+        """Each conditional allOf branch survives schema flattening."""
+        negative = {
+            "if": {"properties": {"type": {"const": "discount"}}},
+            "then": {"properties": {"amount": {"exclusiveMaximum": 0}}},
+        }
+        non_negative = {
+            "if": {"properties": {"type": {"const": "subtotal"}}},
+            "then": {"properties": {"amount": {"minimum": 0}}},
+        }
+        schema = {
+            "type": "object",
+            "properties": {
+                "type": {"type": "string"},
+                "amount": {"type": "integer"},
+            },
+            "allOf": [negative, non_negative],
+        }
+
+        preprocess_schemas.preprocess_full_schema(schema)
+
+        self.assertEqual(schema["allOf"], [negative, non_negative])
+
     def test_preprocess_inlines_entity_fields(self) -> None:
         """The shared entity definition is inlined without its metadata."""
         entity = {