Gluten Free Pizza Muffins

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Using a 12-cup muffin pan or 6-cup jumbo muffin pan, you can make these delicious gluten free pizza muffins. The dough is soft but slightly chewy. Put a couple in your loved one’s lunch box, serve them after school, or when you’re in a hurry at breakfast time.

Mix in your favorite gluten free pizza toppings and/or cheese from the suggestions. I’ve even included brands of dairy free cheese. Then top it with your favorite gluten free pizza sauce or make the recipe I provide. Make it your own!

Gluten Free Pizza Muffins

Prep Time: 30 minutes

Cook Time: 12 minutes

Total Time: 1 hour, 47 minutes

Yield: Makes 6 jumbo and 12 standard muffins

Gluten Free Pizza Muffins

Delicious gluten free pizza muffins, more flavorful than your favorite focaccia.flatbread. Add to a lunch box or serve at home.


  • 1/4 cup water, heated to 100 - 115°F
  • Scant* 1 tablespoon honey, agave, or sugar
  • 1 teaspoon instant yeast
  • 1/2 cup white rice flour, plus more for dusting
  • 1/2 cup potato starch (or more cornstarch)
  • 2 tablespoons cornstarch (or more potato flour)
  • 1 tablespoon crushed red pepper flakes, for heat (or minced sun dried tomatoes) (optional)
  • 1 tablespoon grated Parmesan cheese (or Kraft canister) (or gluten free nutritional yeast + 1/8 teaspoon additional salt, for dairy-free))
  • 1 teaspoon xanthan gum (or guar gum)
  • 1/2 teaspoon fresh minced rosemary
  • 1/4 + 1/8 teaspoon salt
  • 1/4 teaspoon gluten-free baking powder
  • 1/8 teaspoon ground thyme (or 2 teaspoons fresh, minced)
  • 12 slices gluten free pepperoni
  • 12 tablespoons shredded Mozzarella cheese*, plus more for tops
  • 1 large egg, at room temperature, beaten
  • 1/4 cup Gluten Free Pizza Sauce Recipe (or your favorite GF brand including pesto (Buitoni)
  • 2 tablespoons olive oil, plus more for pan
  • 1 tablespoon butter (or oil, for dairy-free), for basting
  • For the Egg Wash:
  • 1 large egg, at room temperature
  • 1 teaspoon water, for basting


  1. Oil the cups of a 6-cup jumbo muffin pan or standard 12-cup muffin pan (or line with muffin papers; set aside.
  2. Add honey to the warm water and stir. Add yeast and stir again. Allow the mixture to rest for at least 5 minutes or until it becomes foamy on top.
  3. In the bowl of your mixer fitted with the whisk/balloon attachment, add white rice flour, potato starch, cornstarch, red pepper flakes (if using), Parmesan cheese, xanthan gum, rosemary, salt, baking powder, and thyme; run on low to combine.
  4. Add small pieces of your favorite meat and/or cheese, about 1 slice of pepperoni per standard muffin (2 for jumbo muffins) and half of the Mozzarella cheese. Add Run the mixer on low to evenly distribute.
  5. In a separate bowl, whisk together eggs, pizza sauce, oil; add to the mixer. Also, add the yeast mixture. Beat on medium speed until smooth (1 minute if using a KitchenAid mixer). The dough should be sticky enough to stick to your hands/fingers. If not, mix in 1 tablespoon of water at a time until it is. Gather the dough into one mound. Set aside to rise in an 80ºF environment for 45 minutes.
  6. Distribute the dough evenly among the 6 cups without smashing the dough down too much. Using wet fingers, smooth out the tops.
  7. Brush the tops with melted butter; set aside to rise for an additional 15 minutes.
  8. While the dough rises, preheat the oven to 475°F.
  9. Whisk together the egg and 1 teaspoon of water; brush on top of the risen muffins. Sprinkle the tops with the remaining Mozzarella;
  10. Bake on the center rack of the oven 14 - 15 minutes for jumbo muffins and 12 minutes for standard muffins, rotating pan mid-baking for even browning if your oven has some hot spots.
  11. Remove the pan from the oven and allow to set in the pan for about 3 minutes. Then transfer the muffins to a wire rack to cool for at least 5 minutes. (If you serve them too soon, they will taste a little gummy.)
  12. If desired, serve with additional pizza sauce.
  13. To store, once completely cool, freeze leftovers in a single layer in gallon-size freezer bags. Defrost muffins in the microwave on low heat or at room temperature. Reheat by microwaving on low or slicing in half and toasting. I even leave them on the dashboard of my car in the sun while I'm driving.



Diced ham and pineapple.

Prosciutto, basil, and fresh Mozzarella.

Bell pepper and onions sautéed in love oil with the cheese of your choosing .

*For dairy-free Mozzarella cheese shreds use Follow Your Heart or Daiya brands.

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