diff --git a/esphome/components/api/api_pb2.h b/esphome/components/api/api_pb2.h
index 033b789c18..a97f6c0a76 100644
--- a/esphome/components/api/api_pb2.h
+++ b/esphome/components/api/api_pb2.h
@@ -322,7 +322,6 @@ enum ZWaveProxyRequestType : uint32_t {
 
 class InfoResponseProtoMessage : public ProtoMessage {
  public:
-  ~InfoResponseProtoMessage() override = default;
   StringRef object_id{};
   uint32_t key{0};
   StringRef name{};
@@ -336,28 +335,29 @@ class InfoResponseProtoMessage : public ProtoMessage {
 #endif
 
  protected:
+  ~InfoResponseProtoMessage() = default;
 };
 
 class StateResponseProtoMessage : public ProtoMessage {
  public:
-  ~StateResponseProtoMessage() override = default;
   uint32_t key{0};
 #ifdef USE_DEVICES
   uint32_t device_id{0};
 #endif
 
  protected:
+  ~StateResponseProtoMessage() = default;
 };
 
 class CommandProtoMessage : public ProtoDecodableMessage {
  public:
-  ~CommandProtoMessage() override = default;
   uint32_t key{0};
 #ifdef USE_DEVICES
   uint32_t device_id{0};
 #endif
 
  protected:
+  ~CommandProtoMessage() = default;
 };
 class HelloRequest final : public ProtoDecodableMessage {
  public:
diff --git a/esphome/components/api/proto.h b/esphome/components/api/proto.h
index c34f7744e6..750fff0810 100644
--- a/esphome/components/api/proto.h
+++ b/esphome/components/api/proto.h
@@ -452,7 +452,6 @@ class DumpBuffer {
 
 class ProtoMessage {
  public:
-  virtual ~ProtoMessage() = default;
   // Default implementation for messages with no fields
   virtual void encode(ProtoWriteBuffer &buffer) const {}
   // Default implementation for messages with no fields
@@ -463,6 +462,11 @@ class ProtoMessage {
   virtual const char *dump_to(DumpBuffer &out) const = 0;
   virtual const char *message_name() const { return "unknown"; }
 #endif
+
+ protected:
+  // Non-virtual: messages are never deleted polymorphically.
+  // Protected prevents accidental `delete base_ptr` (compile error).
+  ~ProtoMessage() = default;
 };
 
 // Base class for messages that support decoding
@@ -482,6 +486,7 @@ class ProtoDecodableMessage : public ProtoMessage {
   static uint32_t count_repeated_field(const uint8_t *buffer, size_t length, uint32_t target_field_id);
 
  protected:
+  ~ProtoDecodableMessage() = default;
   virtual bool decode_varint(uint32_t field_id, ProtoVarInt value) { return false; }
   virtual bool decode_length(uint32_t field_id, ProtoLengthDelimited value) { return false; }
   virtual bool decode_32bit(uint32_t field_id, Proto32Bit value) { return false; }
diff --git a/script/api_protobuf/api_protobuf.py b/script/api_protobuf/api_protobuf.py
index 350947a8d6..9c9cda4d36 100755
--- a/script/api_protobuf/api_protobuf.py
+++ b/script/api_protobuf/api_protobuf.py
@@ -2473,9 +2473,6 @@ def build_base_class(
     out = f"class {base_class_name} : public {parent_class} {{\n"
     out += " public:\n"
 
-    # Add destructor with override
-    public_content.insert(0, f"~{base_class_name}() override = default;")
-
     # Base classes don't implement encode/decode/calculate_size
     # Derived classes handle these with their specific field numbers
     cpp = ""
@@ -2483,6 +2480,8 @@ def build_base_class(
     out += indent("\n".join(public_content)) + "\n"
     out += "\n"
     out += " protected:\n"
+    # Non-virtual protected destructor prevents accidental polymorphic deletion
+    protected_content.insert(0, f"~{base_class_name}() = default;")
     out += indent("\n".join(protected_content))
     if protected_content:
         out += "\n"