by Olena

Gluten Free Muffins

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Olena Osipov

These healthy Gluten Free Muffins with a hint of lemon are tender and moist with a fluffy almond flour interior. Made easy using just 8 natural ingredients, this moist gluten free muffin recipe is naturally refined sugar-free, oil-free, and a delicious breakfast!

Prefer your gluten free muffin recipes with extra add-ins? Why not try these almond flour banana muffins or healthy zucchini muffins!

gluten free muffin dusted with icing sugar and raspberries

My love for almond flour officially has no end in sight. Having recently shared a recipe for almond flour carrot cake and almond flour chocolate cake, – I realized that I’d never shared a plain muffin recipe – well, no more! While almond flour is denser than wheat flour, it has the magical ability to create fluffy, moist, slightly nutty baked treats that taste great and are full of healthy fats and various nutrients.

Even better, these almond flour muffins without banana are also fairly diet-friendly. Not only is this super moist muffin recipe naturally gluten-free (and no-one would guess!), and they are also paleo-friendly, refined sugar-free, oil-free, and grain-free – with just a hint of citrus flavor!

Why This Recipe Works?

  • Simple ingredients mean you can make these almond flour muffins any time.
  • Tender and fluffy thanks to almond flour.
  • Oil free thanks to moisture in Greek yogurt, however almond flour does contain a lot of healthy fats.
  • Wholesome enough to enjoy as a perfect breakfast muffin eaten alone or slathered with a bit of butter – served with a cup of tea (I’m European!) or coffee!
  • Freezer friendly – if you make a double batch, you’ll have breakfast for weeks! Especially if you rotate between them and savory breakfast egg muffins or breakfast casserole (or hashbrown breakfast casserole)!
  • Since this is an excellent ‘base gluten-free muffin recipe’ that also means it’s perfect to experiment with your add-ins of choice: blueberries, chocolate, crushed nuts – there are tons of ways to adapt this moist muffin recipe!

Then again, you can always rotate them with other healthy muffin recipes too; like these healthy carrot muffins, lemon zucchini muffins, morning glory muffins, or chocolate quinoa muffins!

nine gluten free muffins on a kitchen counter

Ingredients and Substitutions

  • Almond flour: Use superfine blanched almond flour for the best results. However, you could also experiment with coarser almond meal – though the texture will be different.
  • Eggs: You’ll need 3 large eggs.
  • 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 muffin recipe since it contains no oil. You could also try the recipe with plain yogurt, but you may need to add up to ¼ cup more flour to achieve the correct thick batter consistency. Alternatively, you could drain your plain yogurt (read recipe notes at the bottom of the post).
  • Baking Powder and Baking Soda: To provide lift and fluffy texture to the gluten-free muffins.
  • Salt: Just a pinch to enhance the cacao 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!

You’ll also need a little cooking spray (I use Misto) for spraying the muffin tin/liners.

eggs, yogurt, almond flour, lemon, baking essentials, vanilla, salt

Optional Add-ins:

  • Flavored yogurt: Technically not an add-in, but you could sub plain yogurt for a flavored Greek yogurt for easily flavored muffins.
  • Chocolate chips: You can use milk, dark, or even sugar-free chocolate chips.
  • Chopped nuts: Walnuts, pecans, almonds, etc. Add about a handful of crushed nuts.
  • Berries: Use fresh or frozen (don’t thaw before baking) blueberries or raspberries (add around 1/2 cup). You might also love these healthy blueberry muffins or this blueberry breakfast cake.
  • Apple: Finely diced apple with a bit of cinnamon makes for a simple adaptation to this gluten-free muffin recipe.
  • Spinach: Okay, stay with me; adding a large handful of spinach to your blender when blending the batter will make green muffins that have extra nutrients and antioxidants but without any spinach flavor! You might need a spoonful or two more almond flour to make up for the liquid content in the spinach.
  • Granulated sugar: 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 granulates sugar alternative) to the tops of the gf muffins before baking.
  • Poppy seeds: 1 tbsp of poppy seeds with lemon zest will make these the best lemon poppy seed muffins!
  • Savory: To adapt this to a savory muffin recipe, you could add a little cheese, sun-dried tomatoes, olives, or even bacon.

How to Make Gluten Free Muffins

  • Preheat the oven: To 350F/125C and line a 12-muffin tin with parchment paper muffin liners. Spray the liners with a bit of cooking spray and then set them aside.
  • Mix the almond muffin batter: In a large bowl, add the eggs, maple syrup, yogurt, vanilla extract, lemon zest, baking soda and powder, and salt. Whisk well to thoroughly combine until there are no lumps. Then, add the almond flour and gently fold it into the muffin batter until 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 for around 22 minutes or until a toothpick inserted in the center comes out mostly clean (with a few crumbs is fine).

Once they’re ready, allow them to cool for around 15 minutes before enjoying!

More Tips for Best Almond Flour Muffins

  • Use liners: I highly recommend using parchment paper muffin liners because almond flour is delicate. The gluten-free muffins tend to stick even to the most well sprayed and even silicone cavities, especially when freshly baked.
  • To make mini muffins: 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.
  • To make homemade almond flour: Use blanched almonds and blend into a floury consistency in 10-second bursts. Optionally sieve the flour, re-blending any chunkier bits.
  • These aren’t meant to be low carb: I love how nutrient-dense and wholesome almond flour baked goods can be, but I didn’t design this moist muffin recipe to be low carb. Feel free to experiment with erythritol but I haven’t tried. Although I have successfully used it to make this almond flour banana bread.

Making GF Muffins Ahead and Storing Instructions

Storing: The gluten-free muffins will store well at room temperature for between 2-3 days. Alternatively, store them within a refrigerator for 5-7 days. As they are very moist, I suggest keeping them loosely covered rather than in an airtight container.

Freeze: Allow the muffins to cool completely before transferring to an airtight container. You can stack the muffins in the container with layers of parchment paper between them. Freeze the gluten-free muffins for up to three months.

Make ahead: Prepare the batter minus the leavening agents up to a day in advance and store covered in the refrigerator. When you want to continue the recipe, add the baking powder and soda, mix well, and then bake as directed.


Can you veganize this gluten free muffin recipe?

With several almond flour bakes that I’ve made, it’s easy to swap out the eggs for chia/flax eggs, and they aren’t quite as fluffy, but it works. However, as this recipe also has yogurt in – I haven’t had a chance to experiment with a dairy-free alternative, so I can’t guarantee results.

I recommend using a dairy-free Greek yogurt alternative if you want to experiment.

For the chia/flax eggs: Mix 3 tbsp of water with 1 tbsp ground chia/flaxseed per egg and allow the mixture to rest for 5-10 minutes to thicken. 

How to drain yogurt?

The main difference between plain and Greek yogurt is the amount of whey in the yogurt (thus how ‘thick’ it is).

To drain your yogurt, simply place a few cheesecloth layers in a colander or use a nut milk bag and spoon in the yogurt, then allow it to drain over a bowl (to use the whey) or the sink until it thickens to your required level.

This can take 12+ hours depending on how thick you want it, so leave time for this – if needed.

Can you reheat the muffins?

Yes, you sure can! You can reheat the gf muffins from chilled or frozen.

From the fridge: Microwave the muffins in 15-second increments until warmed through.
From the freezer:  Add to the microwave and heat in 20-second increments until warmed through. You could also heat them in the oven, wrapped in foil until warmed (about 10-15 mins at 400F when thawed).

More Gluten Free Recipes

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

gluten free lemon muffins
Gluten Free Muffins

Best Ever Gluten Free Muffins

These healthy Gluten Free Muffins with a hint of lemon are tender and moist with a fluffy almond flour interior. Made easy using just 8 natural ingredients, this moist gluten free muffin recipe is naturally refined sugar-free, oil-free, and a delicious breakfast!
Print Save Rate
Course: Muffins and Quick Breads
Cuisine: American Ukrainian
Prep Time: 10 minutes
Cook Time: 22 minutes
Total Time: 32 minutes
Servings: 12 muffins
Calories: 294kcal
Author: Olena Osipov


  • 3 large eggs
  • 1/2 cup maple syrup or honey
  • 1 cup Greek yogurt
  • 1 tsp vanilla extract
  • 1 lemon, lime or orange zest of
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 4 1/4 cups almond flour
  • Cooking spray I use Misto


  • Preheat oven to 350 degrees F. Line 12 muffin tin with parchment paper muffin liners (highly recommended) and spray with cooking spray. Set aside.
    Gluten Free Muffins
  • 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.
    Gluten Free Muffins
  • Add almond flour (make sure to level the top with knife and do not pack) and stir gently with spatula until well mixed.
    Gluten Free Muffins
  • 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.
    Gluten Free Muffins
  • Remove from the oven, let cool for 15 minutes and enjoy.
    Gluten Free Muffins

Make Ahead: You can prepare the batter, minus the leavening agents, up to a day in advance. Leave it covered in the refrigerator and mix in the baking powder and soda before baking the muffins.

    Storing: Store muffins at room temperature for 2-3 days or within the refrigerator for 5-7 days. As they're quite moist, I've found they store better when loosely covered rather than in an airtight container.

      Freezing: Freeze in layers with parchment paper between, in a large freezer bag. They will store in the freezer for up to three 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 (whey). 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. Unless you are an experienced baker, feel free to do so if you can bring batter to the right consistency.
        • Almond meal might work: I am pretty sure it will work, just muffins will be more dense and rise less.
        • Use liners: I highly recommend to use parchment paper muffin liners because almond flour is delicate and muffins to tend to stick even to the most well sprayed and even silicone cavities. Especially when freshly baked.
        • Add poppy seeds: 1 tbsp of poppy seeds will make these best lemon poppy seed muffins.
        Please see Recipe Post for more Tips and FAQs.


        Serving: 1muffin | Calories: 294kcal | Carbohydrates: 21g | Protein: 12g | Fat: 21g | Saturated Fat: 2g | Trans Fat: 1g | Cholesterol: 42mg | Sodium: 197mg | Potassium: 47mg | Fiber: 4g | Sugar: 14g | Vitamin A: 60IU | Vitamin C: 1mg | Calcium: 128mg | Iron: 2mg
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        olena osipov in the studio

        Hello and welcome to iFOODreal.

        My name is Olena Osipov. I'm a mom to 2 boys, a wife to Alex and we reside on magical Vancouver Island in British Columbia, Canada. This is our healthy family recipes blog. Originally from Ukraine, I grew up on real food. As an adult, I struggled with diets for years because none worked long-term. Now for over 10 years, I cook easy healthy meals for my family. I can help you with “What’s for dinner?” too.

        3 comments on “Gluten Free Muffins

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

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