Preheat the oven to 400 degrees F. Line 18 muffin cups with paper liners.
Whisk together the all-purpose and whole-wheat flours with the baking powder, baking soda, cinnamon, nutmeg and salt in a large bowl. Beat the butter, sugar, yogurt, eggs and vanilla together in another large bowl using an electric mixer on medium speed until fluffy. Reduce the speed to low and beat in the flour mixture until combined. Stir in the zucchini and raisins. Divide the batter evenly among the prepared cups.
Bake until a toothpick inserted in the center of the muffins comes out clean, 15 to 18 minutes. Cool the muffins in the pans on a wire rack for 10 minutes; remove from the pans and cool completely on the rack.
When measuring flour, we spoon it into a dry measuring cup and level off the excess. (Scooping directly from the bag compacts the flour, resulting in dry baked goods.)
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