Preheat the oven to 375 degrees F and grease a standard muffin tin well with nonstick spray.
Add the milk, carrot, cheeses, butter, pepperoni (reserving the 2 tablespoons), and egg to a medium bowl. Stir together.
Stir in the flours, baking powder, baking soda, pizza seasoning, and salt.
Divide batter among the prepared muffin tin, using about 1/4 cup in each. Top each with pepperoni.
Bake for 18-20 minutes or until lightly golden brown around the edges and a cake tester inserted into the center comes out cleanly. (There may be some melted cheese on it though!)
Let cool in the pan for 2-5 minutes, then transfer to a wire rack to cool completely. You may need to use a paring knife around the edges of the muffins to help remove them from the pan.
Serve slightly warm.
To store, let cool completely, then store in an airtight container in the fridge for up to 5 days. Heat briefly for 15-30 seconds in the microwave to serve.
To freeze, let cool completely. Transfer to a zip top plastic storage bag, remove as much air as possible, and freeze for up to 3 months. Warm one at a time on a heat-safe plate in the microwave for about 30-60 seconds or until warmed through
Egg-free: Omit eggs. Increase milk to 1 3/4 cups. Increase baking soda to 1 teaspoon. Proceed with the recipe as directed. (They work really well!)
Look for pizza seasoning in the spice aisle. McCormick and Tones make it, and there are specialty brands too like this one that is very good.. It is widely available.
You can make these as mini muffins. You'll want to adjust the timing to 12-14 minutes or until a cake tester inserted into the center comes out cleanly.
You can warm briefly and pack in a thermos for lunch.
Substitute the carrots for broccoli if desired. Just use the tops of the broccoli, avoiding the stems, and finely cut up or chop.
Use all of one type of flour if that's what you have.
Omit the pepperoni to make them vegetarian.
Dice up for younger eaters.
Serve warm. Serve with warm marinara sauce if desired for dipping.