Preheat the oven to 375 degrees F. Grease a 12-cup standard muffin pan with nonstick spray.
In a medium bowl, stir together the flours, baking powder, baking soda, and salt.
In another bowl, stir together the yogurt, maple syrup, eggs, butter, and vanilla.
Gently stir the yogurt mixture into the flour mixture.
Stir in the chocolate chips.
Divide batter among the prepared muffin tin, using about 1/4 cup batter in each cup.
Bake for 14-16 minutes, or until the edges are lightly golden brown and a cake tester inserted into the center comes out cleanly. Remove from oven, then transfer muffins to a wire rack to cool fully.
Once cooled, store in an airtight container for up to 3 days at room temperature. Store in the fridge in an airtight container for up to 5 days. Warm slightly to serve from the fridge. You can also freeze the muffins in a freezer bag with as much air removed as possible for up to 3 months. Thaw at room temperature or in 15 second increments in the microwave.
I like using whole milk Greek yogurt in this recipe. You can use regular style yogurt if you prefer.
Dairy-free: Use a nondairy Greek style yogurt like the plant-based options from Siggis and a neutral oil like canola in place of the butter.
Egg-free: Reduce the yogurt to 3/4 cup. Add 1/4 cup milk and add 1/4 teaspoon additional baking soda.
Gluten-free: Use cup for cup gluten-free all purpose flour.
Dice up as needed for younger eaters.
Top with butter, nut butter, or jam as desired.
Try half chocolate chip and half blueberries, diced strawberries, or diced cherries as a yummy alternative.