Gluten Free Focaccia Muffins (Sourdough Discard Recipe)

If you're like me and think that the golden brown, crunchy crust of focaccia is the best part, you will love these Gluten Free Focaccia Muffins. They’re soft and fluffy on the inside, with a crisp, golden exterior that’s just as satisfying as a full sized focaccia loaf. Perfect for snack time, breakfast, or alongside a meal, these muffins offer all the flavor of traditional focaccia in a mini, easy-to-eat form. Once you try them, you’ll wonder why you ever made focaccia any other way.

Recipe Ingredient Notes

Gluten Free Flour: The only flour I recommend for these gluten free focaccia muffins is Caputo Fioreglut - and trust me, it’s a game-changer. This Italian-imported flour is the secret behind making the best gluten free pizzas and breads. With its super fine texture, Fioreglut has no grittiness or grainy aftertaste, resulting in smooth, well-structured doughs that don’t feel or taste “gluten-free.”

Sourdough Discard: Adding some sourdough discard enhances both the structure and flavor of these muffins. They have a slightly more compact texture compared to my original Gluten-Free Focaccia Recipe. This recipe uses a 50:50 gluten-free sourdough starter, made with equal parts superfine brown rice flour and water. Be sure your discard is at room temperature before using it. If you don’t have any discard on hand, you can substitute it with 40 grams of superfine brown rice flour (or Fioreglut) and 40 grams of water. The focaccia will still be delicious!

Milk Powder: This ingredient is optional. Adding a bit of milk powder helps giving the garlic bread focaccia muffins a golden brown color. If you prefer to keep the muffins dairy-free, you can simply skip it. (Note that non-dairy milk powder won’t have the same effect.)

Active Dry Yeast: I prefer using active dry yeast for this gluten-free focaccia muffin recipe. It does need to be activated in warm liquid before mixing into the dough. If you prefer instant yeast, you can substitute it 1:1. Simply add it directly to the dry ingredients—no activation required. Keep in mind that dough made with instant yeast tends to rise faster, so be sure to watch it closely to prevent over-proofing.

Garlic Bread Toppings: I use a simple garlic butter and chopped parsley along with some grated parmesan to top my gluten free focaccia muffins.

Gluten Free Focaccia Muffin Dough

This foaccia dough is very easy to make. There is no need to bust out your electric mixer or stand mixer. The focaccia dough simply gets mixed with a Danish Dough Whisk or wooden spoon.

1. To activate active dry yeast, heat 275 grams of water in a microwave-safe bowl for 30–60 seconds until it reaches about 110°F. Be careful not to exceed 115°F, as higher temperatures can kill the yeast. For best results, use a digital thermometer to check the temperature.
2. Once the water is warm, sprinkle the yeast and a pinch of sugar over the surface. Let it sit for 10–15 minutes. The yeast is ready when it turns bubbly and frothy. If it doesn’t foam within 10 minutes, it’s likely inactive and should be replaced.

3. Meanwhile, in a mixing bowl, whisk together Caputo Fioreglut Gluten Free Flour, granulated sugar, and kosher salt.
4. Next, add the gluten free sourdough discard and the olive oil, followed by the yeast mixture. Using a Danish dough whisk or a wooden spoon, mix everything together until you have a wet, slightly lumpy dough. It may seem too loose at first, but the flour will absorb the liquid as you mix.
5. Keep stirring until the dough becomes smooth and starts to thicken.

6. Using a flexible spatula, scrape down the sides of the mixing bowl and shape the dough into a ball. It doesn’t have to be perfect - this just makes transferring it easier.
7. Let the dough rest in the bowl for a few minutes to allow the flour to hydrate. Meanwhile, measure out 15 grams of oil and add it to the bottom of your second mixing bowl.
8. After the rest, transfer the dough to the oiled bowl. The oil will help prevent stickiness and make the dough easier to handle.
9. Using the spatula, turn the dough a few times so it’s fully coated in oil, shaping it into a neat dough ball.
10. Cover the bowl with plastic wrap or a clean towel and refrigerate for at least an hour. This slow rise will enhance both the texture and flavor of the dough. Plus, chilled dough is much easier to shape!

Shaping the Focaccia Muffins

I use a Jumbo Muffin Tin to bake these gluten free focaccia muffins. If you are using a standard muffin tin keep in min the muffins will proof and bake faster.

1. Spray a jumbo muffin tin with non-stick cooking spray and set it aside.
2. The foaccia dough should have grown in size and look puffy. If you like you can punch it down before transfering it to a clean kitchen counter. The dough should be oily enough so there is no need to flour the counter.
3. Using a kitchen scale, weigh the entire dough and divide by six - my portions typically weigh around 125 grams each.
4. Gently shape each dough piece into a ball and blob it into the the muffin tin. The dough balls don't have to be perfect and can be shaggy looking.
5. Once all the focaccia muffins are shaped, cover them with a clean tea towel.
6. Let the dough rise in a warm place until they are about 50% larger in size and really puffy looking. Depending on how warm your kitchen or proofing environment is, this can take 45 to 60 minutes. In warm, humid conditions, the dinner rolls will proof more quickly. For a slow proof you can also place them in your refridgerator.

Baking Instructions

1. Around 45 minutes into the proofing process or when the gluten free focaccia muffins start to look really tall and puffy, preheat the oven 400F. A good indiactor that they are getting ready to be baked is when they reach the rim of the muffin tin.
2. Once the oven is fully preheated, top each muffin with a teaspoon of extra virgin olive oil.
3. Use your clean fingers to ‘dimple’ the muffins. Be careful not to press out a lot of the air pockets that have developed during proofing. The dimples are little pockets that fill with oil (think flavor!) during baking. They also give the bread structure and prevent it from rising too much.
4. Top the focaccia muffins with some flaky sea salt and fresh ground pepper amd place it in the fully preheated oven.
5. Bake the jumbo focaccia muffins at 400F for 18-20 minutes until they are golden brown. I highly recommend keeping an eye on them after 18 minutes. Baking times can vary from oven to oven.
6. While the focaccia muffins are baking, finely chop 2 cloves of garlic and a small handful of fresh parsley. Alternatively, you can grate the garlic with a Microplane or use a garlic press.
7. In a small sauté pan, melt the butter over medium-high heat. Add the garlic and sauté for about a minute over medium-low heat until fragrant. Remove from heat and stir in the chopped parsley. If you use dried parsley add it with the garlic to the melted butter so it has a chance to hydrate.
8. Once the gluten free focaccia muffins come out of the oven, generously brush them with the warm garlic butter while they’re still hot.
9. Sprinkle them with additonal fresh chopped herbs and finish with some freshly grated parmesan cheese if you like.
10. Let the muffins cool in the pan for a few minutes before transferring them to a cooling rack or serving platter. Enjoy!

Serving Suggestions

Gluten Free Focaccia Muffins are the best when they are fresh from the oven and still warm and crispy. Just like my Classic Gluten Free Focaccia, these muffins pair well with just about any dish.

Serve them warm alongside soups, stews, or chili to soak up all the delicious flavors. They also pair well with a fresh salad for a light yet satisfying meal. For a heartier option, enjoy them with pasta dishes, especially those with rich tomato or creamy sauces.

Variations of Focaccia Muffins

There are no limits when it comes to topping ideas for gluten free focaccia muffins. Try to abvoid topping them with fresh herbs before baking since they will most likely burn (this is why I choose to do a garlic butter topping after baking).

I have turned this recipe into delicious gluten free pizza focaccia muffins with just a few simple ingredients. Follow the recipe as written and top the fully proofed muffins with your favorite pizza sauce just before baking. Dimple the muffins, pushing some of the pizza sauce inside the muffins. Bake them at 400F for 15 minutes. In the meantime grate some mozarella cheese (the block kind) amd chop up some pepperoni slices.

After 15 minutes, open the oven door and quickly top each muffin with some grated mozzarella and some of the pepperonis. The reason why I cut them into smaller pieces is mainly because they like to slide off. Finish baking the pizza focaccia muffins for an additional 5 minutes, until the cheese is melted and looks bubbly. Carefully remove the muffin pan from the oven and allow the gluten free pizza muffins to cool for a few minutes before serving.

For extra cheesy focaccia muffins, push a few hunks of cheese into the fully proofed muffins when you dimple them. I like to use a cheese that melts beautifully into the dough like mozarella (the block kind) or for some extra flavor a white cheddar. Or whatever your favorite cheese is.

Storage & Freezing

While these focaccia muffins store well for up to 2 days, I highly recommend eating them as quickly as possible. To store them place the fully cooled muffins in an airtight container and store at room temperature.

To freeze focaccia muffins, let them cool completely to room temperature. Freezing them while still warm can create excess moisture and lead to freezer burn. Once cooled, wrap each muffin tightly in plastic wrap to prevent drying out and protect against freezer burn.

After wrapping, place the muffins in a freezer-safe resealable bag or airtight container. Squeeze out as much air as possible to maintain freshness. Label the bag with the date and store the muffins in the freezer for up to 3 months.

When ready to serve, thaw the muffins at room temperature, then warm them in a 300°F (150°C) oven for 10–15 minutes, or until heated through. For extra flavor, brush them with a little melted butter or olive oil before serving to bring back that fresh-from-the-oven taste.

FAQ - Gluten Free Focaccia Muffins

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