Preheat oven to 375ºF.
Combine all-purpose flour, whole wheat flour, sugar, pumpkin pie spice, baking soda, salt and baking powder in medium bowl. Whisk together pumpkin, apple, oil, egg and vanilla in a large bowl. Add dry ingredients, mixing just until moistened. Stir in cranberries and flax seed.
Portion into greased muffin cups or use paper liners. Sprinkle with walnuts. Bake for 20 to 25 minutes or until wooden pick inserted into center comes out clean. Cool in pan on wire rack 5 minutes. Remove from pan to cool completely.