Preheat oven to 350F.
Combine dry ingredients (flour, flax, baking powder, baking soda, salt) in a large bowl and stir with a whisk.
In a separate bowl, lightly beat the eggs and then add the remaining wet ingredients (yogurt, honey, butter or oil, vanilla) and whisk to combine.
Pour wet ingredients into bowl with dry ingredients and stir just until combined and no dry flour remains. Fold in apples and raisins and walnuts, if using.
Spoon batter into greased muffin tins. Bake for 20 minutes or until toothpick inserted in center comes out clean. Enjoy!