Sweet and tender gluten free lemon blueberry muffins feature loads of juicy berries, lemon zest, and an easy gluten-free batter that bakes up perfectly every time. A mix of oat and almond flours plus Greek yogurt creates a gorgeously textured muffin with a soft, plush crumb.

When I'm in the mood to spruce up my gluten free bakery-style blueberry muffins with a hint of bright citrus, I make these gluten free lemon blueberry muffins! Walloped with juicy blueberries and balanced by sweet-tart lemon, these muffins are so flavorful and delicious. I first made these when my oldest daughter was home sick with a cold, and she said they were the best thing she'd eaten in days. If you want even more lemon flavor, drizzle the muffins with a lemon glaze.
Make sure to try my gluten free bluberry muffins or gluten free banana blueberry muffins for other blueberry muffin delights!
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Why This Gluten-Free Muffin Recipe Works
Thanks to the blend of whole grain oat and high-protein almond flour, this recipe creates a smooth-textured muffin that stays fresh for days. Greek yogurt adds additional moisture and ups the protein, so these muffins work double duty as both a snack and an on-the-go breakfast option.
What You'll Love
- So many blueberries. I didn't skimp here - there's a cup and a half of those little beauties, meaning you'll taste them in every bite.
- Rich and flavorful. The Greek yogurt in the batter adds richness and good-for-you protein and fats without being too much. And the lemon zest adds so much brightness.
- Wonderfully textured. Soft yet sturdy and wonderfully moist, these muffins are undetectably gluten-free!

Ingredients Needed
Here's a look at what you'll need to make these lemon blueberry muffins. Make sure to scroll down to my recipe card at the bottom of this post for the full ingredient amounts and instructions!
- Granulated sugar
- Lemon - You'll need the zest of 1 whole lemon to really infuse the muffins with lemon flavor. Try to use an organic lemon if possible!
- Oat flour - Learn how to make oat flour yourself, or pick up a package at the store. Use certified gluten-free oat flour if needed. Or, swap brown rice flour if you don't eat oats.
- Almond flour - I prefer fine-ground almond flour to keep the muffins' crumb light and moist. If you don't eat almonds, substitute more oat flour (like in my oat flour blueberry muffins!), or substitute another nut flour.
- Leavening - A mix of baking powder and baking soda.
- Salt - Fine sea salt or table salt.
- Oil - I used vegetable oil, and any neutral oil, as well as coconut oil, works great.
- Eggs - Use large eggs.
- Greek yogurt - Full-fat, low-fat, or non-fat plain Greek yogurt works fine.
- Blueberries - Feel free to use fresh or frozen blueberries, with no need to defrost the blueberries if using frozen.
Variation Ideas
- Orange zest - Swap the lemon zest for orange zest if you like!
- Add nuts - A ½ cup of chopped walnuts or pecans will add crunch.
- Cinnamon - A classic blueberry muffin often includes a hint of cinnamon. Stir in 1 teaspoon of ground cinnamon for a hint of warmth.

Step-by-Step Instructions
Here's an overview in photos of how to make these sweet muffins:

1. Combine dry ingredients: Rub the lemon zest into the sugar, then whisk in the rest of the dry ingredients.

2. Whisk wet ingredients: Separately, whisk together the wet ingredients, then stir in the dry mix. Fold in the blueberries.

3. Rest: Grease a 12-cup muffin tin, then scoop in the batter and rest it while the oven heats.

4. Bake: Place in a 375F oven and bake for about 20 minutes.

Tips & Recipe Notes
- Grease the muffin tin very well. Muffins that stick to the pan make me so sad! Be sure to really grease the muffin tin with oil or non-stick spray so that the muffins release easily. Or, use muffin liners.
- Rub in the lemon zest. Rubbing the lemon zest into the sugar as the first step is the key to super lemony muffins. This releases the citrus oil and infuses the muffins with flavor.
- Don't substitute for a mix. I know it seems easier, but you'll truly love the texture that comes from the oat and almond flours. If you must, though, give my homemade gluten free flour blend a try.
- Cool completely. As noted, these muffins are very soft straight out of the oven. Let them cool fully so that the crumb sets.
- Make ahead. For a firmer texture, bake the muffins the night before you plan to serve them and store them in an airtight container on the counter.
Proper Storage
Muffins need to be cooled completely before being placed in a container; they get soggy when stored. Then:
- Counter - Place muffins in an airtight container and store them on the counter for up to 3 days.
- Fridge - Place the container in the fridge for up to 5 days.
- Freezer - Transfer muffins to a freezer-safe bag or container and store in the freezer for up to 3 months. Thaw in the fridge before serving.
More Gluten Free Blueberry Recipes
Happy baking! If you make this gluten free lemon blueberry muffins recipe, I'd love to know. Please leave a comment below, reach out with any questions, and tag me on Instagram @Cucina Nicolina ❤️
Recipe

Gluten Free Lemon Blueberry Muffins
Ingredients
- 1 lemon zested
- 1 cup granulated sugar
- 2 cups oat flour (240 grams)
- ¼ cup almond flour (30 grams)
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon fine sea salt
- ¼ cup vegetable oil
- 2 large eggs
- ½ cup Greek yogurt
- 1 ½ cups blueberries fresh or frozen
Instructions
- Preheat the oven to 375°F and grease a 12-cup muffin tin with oil or line it with cupcake liners.
- First, in a large bowl, rub the zest of 1 lemon into 1 cup granulated sugar until fragrant. Whisk in the 2 cups oat flour, ¼ cup almond flour, 1 ½ teaspoons baking powder, ½ teaspoon baking soda, and ½ teaspoon fine sea salt.
- In a medium bowl, the ¼ cup vegetable oil with 2 large eggs an ½ cup Greek yogurt until combined. Whisk and stir in the dry ingredients, then fold in the 1 ½ cups blueberries. The batter will be quite thick.
- Use a ¼ cup measure to scoop the batter into the prepared muffin cups. Rest the batter for 20 minutes.
- Bake the blueberry muffins for 18 to 22 minutes, until a cake tester inserted in the center of one comes out clean. Remove from the oven, cool in the pan for 5 minutes, then turn out onto a rack to cool completely.
Notes
- Grease the muffin tin very well. Muffins that stick to the pan make me so sad! Be sure to really grease the muffin tin with oil or non-stick spray so that the muffins release easily. Or, use muffin liners.
- Rub in the lemon zest. Rubbing the lemon zest into the sugar as the first step is the key to super lemony muffins. This releases the citrus oil and infuses the muffins with flavor.
- Don't substitute for a mix. I know it seems easier, but you'll truly love the texture that comes from the oat and almond flours. If you must, though, give my homemade gluten free flour blend a try.
- Cool completely. As noted, these muffins are very soft straight out of the oven. Let them cool fully so that the crumb sets.
- Make ahead. For a firmer texture, bake the muffins the night before you plan to serve them and store them in an airtight container on the counter.
Nutrition
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