Gluten-Free Lemon Blueberry Muffins (Keto)

These gluten-free lemon blueberry muffins are soft, moist, and bursting with blueberry flavor. Made with almond flour, coconut flour, and naturally sweetened without sugar, they offer all the comfort of a classic bakery muffin while remaining low in carbs and grain-free. Bright lemon zest and juice add a fresh citrus note that pairs beautifully with the juicy blueberries, making these muffins perfect for breakfast, brunch, or an afternoon treat.

A Healthier Version of a Classic Sweet Treat

There are some flavor combinations that never go out of style, and lemon and blueberry (plus a sprinkle of poppy seeds) are one of them. These gluten-free lemon blueberry muffins have become a favorite in my kitchen because they are simple to make, naturally sweetened, and satisfy that craving for a soft, tender muffin without relying on wheat flour or refined sugar.

Made with a combination of almond flour and coconut flour, these muffins are grain-free, low in carbs, and rich in healthy fats and protein. They fit beautifully into a gluten-free, sugar-free, keto-friendly, and lectin-free lifestyle, but most importantly, they are simply delicious. Even people who aren’t following a special diet enjoy them.

The lemon flavor is bright but gentle, allowing the blueberries to shine. Depending on your preference, you can use fewer blueberries for a more pronounced lemon flavor or add a full cup for a juicier, fruit-forward muffin. Fresh or frozen blueberries both work well, making this recipe easy to enjoy year-round.

Whether you’re looking for a healthy breakfast option, a lunchbox treat, or something to enjoy with a cup of coffee or tea, these muffins are a wonderful addition to your recipe collection.

Ingredients

Blueberries

• ½ to 1 cup blueberries (fresh or frozen)

Dry Ingredients

• 1½ cups blanched almond flour, packed
• ¼ cup coconut flour, packed
• 1 tablespoon coconut flour (for coating the blueberries)
• 1 teaspoon baking soda
• ½ teaspoon baking powder
• Pinch of salt

Wet Ingredients

• 3 pasture-raised eggs
• 3 to 4 tablespoons monk fruit sweetener or allulose
• ¼ cup avocado oil or MCT oil
• ¼ cup full-fat coconut milk
• Juice of 2 medium lemons
• Zest of 2 to 3 organic lemons
• 1 teaspoon vanilla extract
• 1 to 2 tablespoons poppy seeds (optional)

How to Make Gluten-Free and Sugar-Free Lemon Blueberry Muffins

Preheat the oven to 175°C (350°F). Line a muffin tin with 10 to 12 paper liners.

Prepare the blueberries. If using fresh blueberries, wash and dry them thoroughly. If using frozen blueberries, pat away any excess moisture. Toss the frozen blueberries with 1 tablespoon coconut flour and set aside, but try not to thaw them. 

In a large bowl, whisk together the almond flour, coconut flour, baking soda, baking powder, salt, and poppy seeds, if using.

In a separate bowl, whisk together the eggs, sweetener, oil, coconut milk, lemon juice, lemon zest, and vanilla extract.

Add the dry ingredients to the wet ingredients and stir until combined. The batter will be thick.

Fold in the blueberries gently, taking care not to overmix.

Divide the batter evenly among the prepared muffin cups, filling each about three-quarters full. Sprinkle with extra poppy seeds if desired.

Bake for 30 to 40 minutes, or until the tops are golden and a toothpick inserted into the center comes out clean. Muffins made with frozen blueberries or a full cup of berries may require closer to 40 minutes.

Allow the muffins to cool in the pan for 10 minutes before transferring them to a wire rack to cool completely.

Tips & Notes for a Successful Bake

Why coat the blueberries?

Coating the blueberries in coconut flour helps absorb excess moisture and prevents them from sinking to the bottom of the muffins.

Fresh vs. frozen wild blueberries

Both fresh and frozen wild blueberries work beautifully in this recipe, but they produce slightly different results. Fresh blueberries, especially the larger cultivated varieties commonly found in grocery stores, hold their shape well during baking and release less moisture. They create lighter-colored muffins with more distinct pockets of fruit.

Frozen wild blueberries are smaller, juicier, and more intensely flavored. As they bake, they release more moisture into the batter, resulting in softer, moister muffins with a deeper blueberry flavor and a darker purple hue throughout. If using frozen wild blueberries, expect the baking time to be slightly longer.

Neither option is better — it simply depends on whether you prefer a lighter, more lemon-forward muffin or a richer, more intensely blueberry-flavored one.

Measuring the flour

For best results, lightly spoon the flour into the measuring cup and then gently press it down until full. Almond flour and coconut flour can vary significantly in volume, and using too little flour may result in muffins that are overly moist.

Sweetness level

These muffins are only lightly sweetened. If you prefer a sweeter muffin, increase the sweetener to 4 tablespoons.

Storage

Store in an airtight container in the refrigerator for up to 5 days, or freeze for longer storage. They thaw beautifully and make a convenient grab-and-go breakfast.

More sugar-free desserts

This recipe is part of our 30+ Healthy Sugar-Free Dessert Recipes round-up. Check it out for a selection of my favorite sugar-free sweet treats that are also gluten-free and lectin-free.

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