A gluten-free focaccia pizza muffin torn open to show the soft, airy interior with tomato sauce and melted cheese on top.

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

Same amazing dough, new twist. If you’ve made my gluten-free focaccia before, you already know the magic of Caputo Fioreglut flour. That same soft, airy texture and golden, crispy edge shines here — just in a muffin pan!
Easy to make. You don’t need to be a professional baker to pull these off — the dough is easy to handle, the results are impressive, and you can customize each muffin with your favorite toppings.
Endlessly customizable. Everyone can top their own — classic cheese, pepperoni, roasted vegetables, or even BBQ chicken. It’s like personal pizzas, but with the rich flavor and olive oil crunch of focaccia.

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

Side angle of gluten-free focaccia pizza muffins showing crisp, golden edges and melted cheese on top.

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.

Muffin pan brushed with olive oil, ready for gluten-free focaccia dough portions.

Grease the muffin pan generously with olive oil.
Make sure the bottoms and sides are well coated — this helps the muffins crisp up and release easily after baking. Portioned balls of gluten-free focaccia dough placed in an oiled muffin tin before rising.

Portioned balls of gluten-free focaccia dough placed in an oiled muffin tin before rising.

Portion the dough into the muffin tin.
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. Risen gluten-free focaccia dough in muffin cups after proofing, ready to be topped.

Risen gluten-free focaccia dough in muffin cups after proofing, ready to be topped.

Cover the muffin tin lightly with plastic wrap or a clean towel so the dough doesn’t dry out. As it rises, it should puff up and dome slightly over the top of each cup. When my kitchen is cold, I set the pan in the oven with the light on (but the oven off) so it stays warm while the dough proofs. Risen focaccia dough dimpled with olive oil and sprinkled with Italian seasoning and flaky salt.

Risen focaccia dough dimpled with olive oil and sprinkled with Italian seasoning and flaky salt.

Dimple the dough and drizzle with olive oil.
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. Muffin tin filled with focaccia dough topped with pizza sauce and shredded mozzarella cheese before baking.

Muffin tin filled with focaccia dough topped with pizza sauce and shredded mozzarella cheese before baking.

Add the pizza toppings and dimple again to push some of the sauce and cheese into the dough so it bakes together and doesn’t just sit on top. Golden brown gluten-free focaccia pizza muffins just baked in the pan, topped with melted cheese and herbs.

Golden brown gluten-free focaccia pizza muffins just baked in the pan, topped with melted cheese and herbs.

Bake until golden and bubbly. Cool them in the pan for a few minutes before removing.

Expert Tips

Use lots of oil. Gluten-free doughs behave differently than traditional wheat doughs — this one will feel sticky, more like cookie dough than bread dough. Oil your hands (not flour them!) to portion out the dough without sticking.
Keep an eye on the rise. Room temperature can affect how quickly your dough doubles. In a warm kitchen, it may only take 45 minutes. In a cooler one, closer to 75 minutes. Look for a soft, puffed dough that fills the wells about three-quarters full.
Hosting hack: Set out a few topping bowls (mozzarella, pepperoni, roasted peppers, olives) and let everyone build their own before baking. It’s interactive and so fun for casual get-togethers.

Recipe FAQs

Can I use a different gluten-free flour blend?

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.