Preheat oven to 350 degrees F (175 degrees C). Spray 12 muffin cups with cooking spray.
Mix the flour, baking powder, baking soda, and salt in a bowl.
In another bowl, stir together the butter, egg, milk, zucchini, and garlic until well blended. Mix the flour mixture into the milk mixture, about 1/2 cup at a time, stirring between additions, until the flour mixture is incorporated. Fold in the Cheddar cheese, Parmesan cheese, and crumbled bacon, and pour the batter into the prepared muffin cups.
Bake in the preheated oven until a toothpick inserted into the center of a muffin comes out clean, 30 to 35 minutes. Allow muffins to cool slightly before removing from muffin cups; serve warm. Refrigerate leftovers.
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