diff --git a/src/cobra/core/gene.py b/src/cobra/core/gene.py
index 56733ec46..5c0d90963 100644
--- a/src/cobra/core/gene.py
+++ b/src/cobra/core/gene.py
@@ -221,6 +221,19 @@ def __init__(self, id: str = None, name: str = "", functional: bool = True) -> N
         super().__init__(id=id, name=name)
         self._functional = functional
 
+    @property
+    def id(self) -> str:
+        return super().id
+
+    @id.setter
+    def id(self, new_id) -> None:
+        warnings.warn(
+            "Direct modification of gene.id is discouraged and can lead to unexpected gene duplications. "
+            "Use cobra.manipulation.modify.rename_genes to safely rename genes.",
+            UserWarning
+        )
+        super(Gene, self.__class__).id.fset(self, new_id)
+    
     @property
     def functional(self) -> bool:
         """Flag indicating if the gene is functional.