Almond Flour Yogurt Muffins are tender, moist, and fluffy with a light hint of lemon. Made with only 8 ingredients, these healthy muffins are also gluten free.

Prefer your almond flour muffins with extra add-ins? Why not try these almond flour banana muffins, almond flour zucchini muffins, or almond flour blueberry muffins.

Almond flour yogurt muffins in paper liners with fresh raspberries.

My love for baking with almond flour officially has no end in sight!

These almond flour yogurt muffins are so simple to make! Made in one bowl and ready in just over 30 minutes, they are light and fluffy plus you can jazz them up for a new snack or breakfast muffin on a weekly basis.

Ingredients in Almond Flour Yogurt Muffins

Almond flour, Greek yogurt, maple syrup, eggs, baking staples and vanilla extract ingredients.
  • Almond flour: Use superfine blanched almond flour for the best light muffin texture results. Almond meal could be used but almond flour yogurt muffins will be more dense and rise less.
  • Eggs: You’ll need 3 large eggs, since this recipe does not have gluten they help bind the almond flour muffins.
  • Sweetener: Maple syrup or honey will work. Other liquid sweeteners may also work but the flavor will vary. For a sugar free option, feel free to experiment using a sweetener like erythritol.
  • Greek yogurt: Will yield a wonderfully moist almond flour yogurt muffin recipe since it contains no oil. You could also try the recipe with plain Instant Pot yogurt, but you may need to add up to 1/4 cup more flour to achieve the correct thick batter consistency. Alternatively, you could drain your plain yogurt. Flavored yogurt could be used for a sweeter almond flour muffin.
  • Baking powder and baking soda: To provide lift and fluffy texture.
  • Salt: Just a pinch to enhance the overall flavor.
  • Vanilla extract: Or vanilla paste will work.
  • Citrus zest: You can use the zest of one lemon, lime, or orange. Don’t omit it, as the difference it makes in flavor is definitely noticeable!
Unwrapped almond flour muffin that has a bite taken out of it.

Why Use Almond Flour in Baking?

While almond flour is denser than wheat flour, it has the magical ability to create fluffy, moist, slightly nutty baked treats that taste great.

For gluten free baked goods, it doesn’t get much easier than using one ingredient almond flour! It’s grain free, lower in carbs than traditional white flour, and full of healthy fats and various nutrients including Vitamin E and magnesium.

How to Make Almond Flour Yogurt Muffins

Here is how to make almond flour yogurt muffins just in one bowl. Full recipe card is below.

Mix wet ingredients and baking staples – In a large bowl, add the eggs, maple syrup, yogurt, vanilla extract, lemon zest, baking soda, baking powder, and salt. Whisk well to thoroughly combine until there are no lumps.

Fold in almond flour gently – Use a spatula to stir to combine ingredients until muffin batter is well incorporated.

Bake the muffins – Use an ice cream scoop to divide the muffin batter between the 12 muffin liners, then bake in the oven on the middle rack at 350 F degrees for around 22 minutes or until a toothpick inserted in the center comes out mostly clean (with a few crumbs is fine).

Cool and enjoy – Once almond flour yogurt muffins are ready, allow them to cool for around 15 minutes before enjoying!

Tips For Best Results

  • I highly recommend using parchment paper muffin liners because almond flour is delicate. The almond flour muffins tend to stick even to the most well sprayed and even silicone cavities, especially when freshly baked.
  • Use a good quality almond flour that is not gritty. If you are having trouble finding almond flour, you can make homemade almond flour easily.
  • Do not substitute the almond flour for another flour. The recipe has not been tested as such and I cannot vouch for results. Browse my list of healthy muffin recipes for other flour options.
  • Do not skip the zest, it adds a depth of light flavor that really makes these almond flour yogurt muffins light and delicious!
  • If you’ve got a sweet tooth and aren’t used to more subtle baked goods, feel free to sprinkle a tiny amount of granulated sugar (or a granulated sugar alternative) to the tops of the muffins before baking.
Almond flour yogurt muffins dusted with icing sugar.

Flavor Variations

Since this is an excellent base almond flour muffin recipe that also means it’s perfect to experiment with your add-ins of choice. Blueberries, chocolate, crushed nuts you name it, there are tons of ways to adapt this moist almond flour yogurt muffin recipe for breakfast!

  • Chocolate chips: You can use milk, dark, or even sugar free chocolate chips. Try these banana protein muffins with almond flour and chocolate chips!
  • Chopped nuts: Walnuts, pecans, or almonds. Add about a handful of crushed nuts.
  • Berries: Use 1/2 cup fresh or frozen blueberries or raspberries (don’t thaw before baking).
  • Lemon poppyseed: Add 1 tablespoon of poppy seeds with lemon zest.

How to Store

Let the muffins cool completely before storing them loosely covered at room temperature for 2-3 days or store within a refrigerator 5-7 days. Store in the freezer up to 3 months.

Storage Tip

If you would like to learn more about making your leftover muffins stay fresh longer, check out my posts how to store muffins and how to freeze muffins.


Can I make vegan almond flour yogurt muffins?

Unfortunately not. Almond flour is gluten-free flour that relies on a lot of eggs as a binder. Your vegan muffins will come out very flat and dense.

Can I make these into mini muffins?

Yes. You’ll just need to reduce the baking time. I suggest checking on them after 10 minutes until an inserted toothpick comes out almost clean.

Can I substitute sour cream for Greek yogurt?

Since both are naturally acidic this should work fine, nutritional information will change.

More Muffin Recipes to Try

You might also enjoy this list of 20 almond flour recipes, which are all naturally gluten free!

Looking down at almond flour yogurt muffins dusted with icing sugar and raspberries around them.
gluten free muffins

Almond Flour Yogurt Muffins

Almond Flour Yogurt Muffins with a hint of lemon are gluten free, refined sugar free and oil free. Only 8 ingredients and made in one bowl.
5 from 16 votes
Servings 12 muffins
Calories 294
Diet Gluten Free
Prep Time 10 minutes
Cook Time 22 minutes
Total Time 32 minutes



  • Preheat oven to 350 degrees F. Line 12 muffin tin with parchment paper muffin liners (highly recommended) and spray with cooking spray. Set aside.
  • In a large bowl, add eggs, maple syrup, yogurt, vanilla extract, lemon zest, baking powder, baking soda and salt. Whisk very well until combined and no lumps.
  • Add almond flour (make sure to level the top with knife and do not pack) and stir gently with spatula until well mixed.
  • Using an ice cream scoop, divide batter (each scoop will be heaping) between 12 openings of previously prepared muffin tin. Bake for 22 minutes on the middle rack or until toothpick inserted in the center comes out clean.
  • Remove from the oven, let cool for 15 minutes and enjoy.



  • Store: Store muffins at room temperature loosely covered for 2-3 days or within the refrigerator for 5-7 days. 
  • Freeze: Freeze in a large freezer bag for up to 3 months.
  • Regular yogurt: You can use plain regular (not Greek) yogurt, however might have to add 1/4 cup extra almond flour since it contains more liquid. Can also use flavored yogurt. The goal is to bring batter to consistency in the photos – thicker than for pancakes.
  • Don’t use dry sweetener: If you use dry sweetener, batter consistency will be offset. 
  • Almond meal might work: I am pretty sure it will work, just muffins will be more dense and rise less.
  • Use liners: Almond flour is delicate and muffins to tend to stick even to the most well sprayed and even silicone cavities. Especially when freshly baked.


Serving: 1muffin | Calories: 294kcal | Carbohydrates: 21g | Protein: 12g | Fat: 21g | Saturated Fat: 2g | Trans Fat: 1g | Cholesterol: 42mg | Sodium: 197mg | Fiber: 4g | Sugar: 14g
Course: Muffins and Quick Breads
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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    1. Berries: Use 1/2 cup fresh or frozen blueberries or raspberries (don’t thaw before baking). Any other fruit you were thinking about? I just wouldn’t add more than 1/2 cup.

  1. 5 stars
    I made these and they are delicious, I did ad a little lemon juice as well. Made them in my camper oven had to cook them longer but still turned out perfect!

  2. 5 stars
    These were fabulous! Thanks for a great recipe. I did make one minor tweak, couldn’t help myself, and along with the lemon zest, added the juice of 1/2 of a lemon. I’d have used the whole lemon but did not want to add too much moisture. Anyway, these were fantastic, and a real hit for the family. Oh and yes, I also threw in mini chocolate chips. Perfect!

    1. That’s so great! It sounds like you have a new favorite, Jennie! You could use the juice of whole lemon, muffins will be fine.

  3. 5 stars
    Thank you for the great recipe!!❤️All I had were the ingredients that you had listed. (I scoured the internet looking for a cookie recipe with almond flour and Greek yogurt and I found your muffin recipe!) I made the muffins first with the honey like you suggested, they were terrific! And then I decided to be brave and use the same recipe to make cookies but with maple syrup (like you suggest) added some almond extract as well as the vanilla and I threw some chocolate chips in it. They turned out great as well!! The whole family loved them they were fluffy and moist but also had a nice semi-hard shell. And you are absolutely right about using lemon zest it made the muffins and cookies perfect. For the holidays I’m thinking about throwing some cranberries in the recipe to see how it goes 😁

  4. 5 stars
    They are very tasty but mine looked more like biscuits and were burning a little on the tops

    Not sure if I did something wrong

  5. Could I reduce the maple syrup to 1/4 cup? If so would I make any other changes to the recipe? Thanks!

5 from 16 votes (8 ratings without comment)

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