diff --git a/chromadb/api/types.py b/chromadb/api/types.py
index 3cfc2c84301..965e4bd0ec0 100644
--- a/chromadb/api/types.py
+++ b/chromadb/api/types.py
@@ -42,6 +42,11 @@
     "UpdateMetadata",
 ]
 META_KEY_CHROMA_DOCUMENT = "chroma:document"
+# Define reserved operator names
+RESERVED_OPERATORS = [
+    "$and", "$or", "$in", "$nin", "$gt", "$gte", "$lt", "$lte", "$ne", "$eq"
+]
+
 T = TypeVar("T")
 OneOrMany = Union[T, List[T]]
 
@@ -682,6 +687,18 @@ def validate_metadata(metadata: Metadata) -> Metadata:
             raise ValueError(
                 f"Expected metadata to not contain the reserved key {META_KEY_CHROMA_DOCUMENT}"
             )
+        # Add validation for operator names used as metadata keys
+        if key in RESERVED_OPERATORS:
+            raise ValueError(
+                f"Metadata key '{key}' conflicts with a reserved operator name. "
+                f"Please use a different key name."
+            )
+        # Validate that strings starting with $ aren't used for metadata keys
+        if isinstance(key, str) and key.startswith("$"):
+            raise ValueError(
+                f"Metadata key '{key}' starts with '$', which is reserved for operators. "
+                f"Please use a different key name."
+            )
         if not isinstance(key, str):
             raise TypeError(
                 f"Expected metadata key to be a str, got {key} which is a {type(key).__name__}"
diff --git a/chromadb/segment/impl/metadata/sqlite.py b/chromadb/segment/impl/metadata/sqlite.py
index 22544f1948f..dc46c68436f 100644
--- a/chromadb/segment/impl/metadata/sqlite.py
+++ b/chromadb/segment/impl/metadata/sqlite.py
@@ -538,6 +538,17 @@ def _where_map_criterion(
                     for w in cast(Sequence[Where], v)
                 ]
                 clause.append(reduce(lambda x, y: x | y, criteria))
+            # Add explicit checks for $in and $nin operators at top level
+            elif k == "$in" or k == "$nin":
+                # Handle $in and $nin operators when they are at the root of a where clause
+                # This ensures they are treated as operators, not metadata keys
+                expr = cast(Union[LiteralValue, Dict[WhereOperator, LiteralValue]], v)
+                # We pass an empty string as the key and the operator as a parameter to _value_criterion
+                if isinstance(v, list):
+                    clause.append(_value_criterion("", v, cast(InclusionExclusionOperator, k), q, metadata_t, embeddings_t))
+                else:
+                    # Handle other value types
+                    clause.append(_value_criterion("", [v], cast(InclusionExclusionOperator, k), q, metadata_t, embeddings_t))
             else:
                 expr = cast(Union[LiteralValue, Dict[WhereOperator, LiteralValue]], v)
                 clause.append(_where_clause(k, expr, q, metadata_t, embeddings_t))
diff --git a/test_reproduce/test_complex_operator_bug.py b/test_reproduce/test_complex_operator_bug.py
new file mode 100644
index 00000000000..43579b722f4
--- /dev/null
+++ b/test_reproduce/test_complex_operator_bug.py
@@ -0,0 +1,68 @@
+import pytest
+import chromadb
+import json
+
+def test_complex_metadata_operator_bug():
+    """
+    This test demonstrates a critical bug in Chroma's metadata filtering when metadata keys match operator names.
+    
+    The issue occurs with complex where clauses that could be ambiguously interpreted.
+    """
+    client = chromadb.Client()
+    collection = client.create_collection("test_collection_complex")
+    
+    # Setup test documents
+    collection.add(
+        ids=["id1", "id2", "id3", "id4"],
+        documents=["doc1", "doc2", "doc3", "doc4"],
+        metadatas=[
+            {"$in": "value1", "category": "A"},           # Has a key that matches operator
+            {"category": "A", "tag": "special"},          # Normal metadata, category A
+            {"$in": "value3", "category": "B"},           # Has a key that matches operator, different category
+            {"category": "B", "tag": "special"}           # Normal metadata, category B
+        ]
+    )
+    
+    print("=== Test: Complex filtering showing operator name ambiguity bug ===")
+    
+    # The critical test: filter for category B documents using "$in" as a METADATA KEY
+    # and simultaneously filter for "tag" being in a list using $in as an OPERATOR
+    try:
+        bug_result = collection.get(
+            where={"$and": [
+                {"$in": "value3"},  # Looks for documents where metadata key "$in" equals "value3"
+                {"category": "B"},   # Looks for documents where "category" is "B"
+                {"tag": {"$in": ["special"]}}  # Uses $in as an operator to match "tag" in list
+            ]}
+        )
+        
+        print(f"Result of query trying to find documents with key '$in'='value3' AND category='B' AND tag in ['special']:")
+        print(json.dumps(bug_result, indent=2))
+        
+        # Check if we get the expected result (should be only id4)
+        # But due to the bug, the system may get confused with the "$in" usage
+        if len(bug_result["ids"]) == 1 and bug_result["ids"][0] == "id4":
+            print("✅ Query worked correctly, found the right document")
+        else:
+            print(f"❌ BUG CONFIRMED: Query returned incorrect results: {bug_result['ids']}")
+            print("   Expected only id4, as it's the only one with category B AND tag 'special'")
+            if len(bug_result["ids"]) == 0:
+                print("   Got no results - system likely confused by '$in' appearing both as metadata key and operator")
+    
+    except Exception as e:
+        print(f"❌ Error with complex query: {e}")
+        print("BUG CONFIRMED: System cannot handle complex queries with operator names as metadata keys")
+    
+    # Compare with a reference query that doesn't use "$in" as a metadata key
+    ref_result = collection.get(
+        where={"$and": [
+            {"category": "B"},
+            {"tag": {"$in": ["special"]}}
+        ]}
+    )
+    
+    print("\nReference query without using '$in' as metadata key:")
+    print(json.dumps(ref_result, indent=2))
+
+if __name__ == "__main__":
+    test_complex_metadata_operator_bug()