These gluten-free focaccia pizza muffins take everything you love about pizza night and wrap it up in a bakery-style muffin shape. Made with my tried-and-true gluten-free focaccia dough, they’re rich with olive oil and have that signature chewy texture that Caputo Fioreglut is famous for.
They do take some time to rise — but I promise, the process is simple and the results are so satisfying. Whether you serve them warm for dinner, pack them for lunch, or make them part of a build-your-own pizza night, these focaccia muffins are endlessly versatile. I went classic with mozzarella and parmesan, but you can let everyone pick their own toppings — pepperoni, roasted veggies, or even a little spicy honey drizzle.
Why You’ll Love this Recipe
Searching for more gluten-free focaccia recipes? Gluten-Free Pumpkin Focaccia / Gluten-Free Focaccia Pizza / Gluten-Free Blueberry Crumble Focaccia / Gluten-Free Chicago Hot Dog Focaccia
Ingredients
TIP
Don’t be shy with the olive oil! That generous drizzle before baking is what gives each muffin its crisp, golden edges — just like the best focaccia bakery loaves.
Searching for more gluten-free dinner recipes? spinach feta egg muffins / gluten-free breakfast casserole / gluten-free mini quiches
Ingredient Notes
- Caputo Gluten-Free Flour – This recipe will ONLY work with this flour blend and is the secret to that bakery-style focaccia texture — chewy, springy, and never gummy. It’s made with gluten-free wheat starch that’s tested to below 20ppm, so it’s safe for most people with celiac disease. However, if you have a wheat allergy, do not use or make this recipe.
- Instant Yeast – Use instant or rapid-rise yeast, not active dry. It can go straight into the dry ingredients without proofing first, which keeps the process simple and reliable.
- Sugar – A tablespoon might sound like a lot, but it doesn’t make the dough sweet. The sugar feeds the yeast and helps the crust brown beautifully.
- Olive Oil – Olive oil gives the dough richness and that signature crisp edge. Use a good-quality extra-virgin olive oil, and don’t be shy with it. You’ll need it in the dough, in the pan, and brushed on top before baking.
- Pizza Sauce – Pick a sauce you love since it’s the main flavor layer here. I used Mutti pizza sauce for mine.
How to Make Pizza Focaccia Muffins
For the ingredient list with measurements, full instructions, printable recipe, and additional notes, please scroll down to the recipe card.
Make sure the bottoms and sides are well coated — this helps the muffins crisp up and release easily after baking.
Each cup should be about halfway to three quarters of the way full. The dough will feel soft and slightly sticky, which is what you want. Lightly oil your hands to make this step easier.
Press gently with your fingertips to create small indents across the top. The dimples hold the olive oil and seasoning, giving the focaccia its signature texture and flavor.
Expert Tips
Recipe FAQs
This recipe was developed specifically for Caputo Fioreglut, which gives the dough its soft, springy texture. Other blends will change the structure completely, so I don’t recommend substituting.
Storage instructions
Pizza focaccia muffins are best the day they are made, but we have stored them before for some quick lunches the next few days.
Refrigerator Storage
Keep leftover muffins in an airtight container in the refrigerator for up to 2-3 days. To bring back that crisp edge, reheat them in a 350°F oven or air fryer for 4 to 8 minutes instead of the microwave.
Freezer Storage
Let the muffins cool completely. Freeze them in a single layer on a baking sheet until solid, then transfer to a freezer-safe bag or container. They’ll keep well for about 3 months.
Reheat from Frozen
Place frozen muffins on a parchment-lined baking sheet and warm in a 350°F oven for 10 to 12 minutes, until heated through and the cheese is melty again.
Make Ahead
You can prepare the dough up to 12 hours in advance. After mixing, portion it into the oiled muffin wells, cover tightly with plastic wrap, and refrigerate overnight for up to 12 hours. When you’re ready to bake, let the pan sit at room temperature to finish the rise for about 30 minutes before dimpling, adding toppings and baking as directed.
More gluten-free bread and rolls to try
Did you make this recipe?
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Gluten-Free Pizza Focaccia Muffins
Ingredients
For the Dough
- 520 g (about 4 cups) Caputo Fioreglut Gluten-Free Flour - you cannot use any other flour blend with this recipe
- 12 g (about 4 teaspoons) instant yeast
- 12.5 g (1 tablespoon) granulated sugar
- 12 g (2 teaspoons) kosher salt
- 480 g (2 cups) warm water - (120–130°F)
- 42 g (3 tablespoons) extra-virgin olive oil - for the dough – extra will be needed for greasing and topping as noted below
For the Pan
- 56 g (1/4 cup) extra-virgin olive oil - divided between muffin tins
For the Toppings
- 2 tablespoons extra-virgin olive oil
- 2 teaspoons Italian seasoning
- 1 teaspoon flaky sea salt - such as maldon salt
- 1 cup (250g) pizza sauce
- 2 cups shredded mozzarella cheese
- 2 tablespoons freshly grated parmesan cheese - or to taste
**Use the toggle button above to turn the instruction photos on and off!
Instructions
- Make the dough. In a large mixing bowl, combine 520g (4 cups) Caputo Fioreglut gluten-free flour, 12g (2 teaspoons) kosher salt, 12g (4 teaspoons) instant yeast, and 12.5g (1 tablespoon) sugar. Add 480g (2 cups) warm water and 42g (3 tablespoons) olive oil. Mix with a spatula until a thick, sticky dough forms. Set aside for a few minutes while you prepare the muffin tins.
- Prepare the pans. Brush two 12-cup muffin tins generously with about 56g (¼ cup) olive oil (about 1/2 teaspoon in each muffin well), coating the bottoms and sides evenly. The oil creates crisp, golden edges and helps the muffins release easily after baking.
- Portion and rise. Divide the dough into 24 equal portions, about 45g each, and place one into each oiled muffin cup. Brush the tops lightly with olive oil. Cover loosely with plastic wrap or a clean towel and let rise until puffy and domed, about 1 hour. When my kitchen is cold, I set the pans in the oven with the light on (but the oven off) so they stay warm while the dough proofs.
- Dimple and season. Once risen, gently dimple each portion with your fingertips. Drizzle with remaining 2 tablespoons olive oil and sprinkle evenly with 2 teaspoons Italian seasoning and 1 teaspoon flaky sea salt.
- Add toppings and dimple again. Spoon pizza sauce over each muffin and top with shredded mozzarella. Gently press with your fingertips to push some of the sauce and cheese into the dough so it bakes together.
- Bake. Bake at 425°F (220°C) for 18 to 20 minutes until golden brown with crisp edges and bubbling cheese. Rotate the pans halfway through baking for even color.
- Cool and serve. Let the muffins rest in the pan for 5 minutes before removing. Top with freshly grated parmesan and an extra drizzle of olive oil, if desired. Serve warm.
Notes
- Flour note: Caputo Fioreglut contains gluten-free wheat starch, which is safe for people with celiac disease but not suitable for those with a wheat allergy. If you use a different blend, expect a very different result in both texture and structure.
- I always recommend baking by weight, especially with gluten-free flours. But for convenience, I’ve included volume measurements too.
- Always be sure to double check all of your ingredients to confirm they are gluten-free.
Nutrition
