diff --git a/gateway/mcp.go b/gateway/mcp.go
index ecd37d700..2fb132b84 100644
--- a/gateway/mcp.go
+++ b/gateway/mcp.go
@@ -572,7 +572,45 @@ func projectMCPMarkedValue(value reflect.Value) (interface{}, bool) {
 	}
 	marker := value.FieldByName("Has")
 	if !marker.IsValid() || marker.Kind() != reflect.Ptr || marker.IsNil() || marker.Elem().Kind() != reflect.Struct {
-		return mcpJSONValue(value), false
+		// A discriminated wrapper can contain marked patches without owning
+		// a marker itself. Preserve the wrapper's JSON shape while projecting
+		// its marked children before omitempty can erase explicit clears.
+		if implementsMCPJSONMarshaler(value.Interface()) {
+			return mcpJSONValue(value), false
+		}
+		normalized, ok := mcpJSONValue(value).(map[string]interface{})
+		if !ok {
+			return mcpJSONValue(value), false
+		}
+		marked := false
+		for index := 0; index < value.NumField(); index++ {
+			field := value.Type().Field(index)
+			if !field.IsExported() {
+				continue
+			}
+			name := strings.Split(field.Tag.Get("json"), ",")[0]
+			if name == "-" {
+				continue
+			}
+			projected, childMarked := projectMCPMarkedValue(value.Field(index))
+			if !childMarked {
+				continue
+			}
+			if field.Anonymous && name == "" {
+				if embedded, ok := projected.(map[string]interface{}); ok {
+					for key, item := range embedded {
+						normalized[key] = item
+					}
+				}
+			} else {
+				if name == "" {
+					name = field.Name
+				}
+				normalized[name] = projected
+			}
+			marked = true
+		}
+		return normalized, marked
 	}
 	marker = marker.Elem()
 	return projectMCPMarkedStruct(value, marker), true
diff --git a/gateway/mcp_wrapped_presence_test.go b/gateway/mcp_wrapped_presence_test.go
new file mode 100644
index 000000000..f4a3ebcfd
--- /dev/null
+++ b/gateway/mcp_wrapped_presence_test.go
@@ -0,0 +1,36 @@
+package gateway
+
+import (
+	"encoding/json"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestMCPBodyPreservesWrappedPatchClears(t *testing.T) {
+	type presence struct {
+		ID, Tags, Nullable, Omitted bool
+	}
+	type patch struct {
+		ID       int       `json:"id"`
+		Tags     []string  `json:"tags,omitempty"`
+		Nullable *string   `json:"nullable,omitempty"`
+		Omitted  string    `json:"omitted,omitempty"`
+		Has      *presence `json:"-"`
+	}
+	type wrapper struct {
+		Kind  string `json:"kind"`
+		Patch *patch `json:"patch,omitempty"`
+	}
+	input := []wrapper{{Kind: "native", Patch: &patch{
+		ID: 7, Tags: []string{}, Has: &presence{ID: true, Tags: true, Nullable: true},
+	}}}
+	encoded, err := json.Marshal(preserveMCPBodyPresence(nil, input))
+	require.NoError(t, err)
+	require.JSONEq(t, `[{"kind":"native","patch":{"id":7,"tags":[],"nullable":null}}]`, string(encoded))
+	// Unmarked models retain their existing omitempty behavior.
+	input[0].Patch.Has = nil
+	encoded, err = json.Marshal(preserveMCPBodyPresence(nil, input))
+	require.NoError(t, err)
+	require.JSONEq(t, `[{"kind":"native","patch":{"id":7}}]`, string(encoded))
+}