Almond Flour Blueberry Yogurt Muffins

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This gluten-free and low-carb Almond Flour Blueberry Muffin is the perfect replacement for your favorite bakery blueberry muffin. Easy to make, packed with protein, and no special ingredients needed.

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Almond Flour Blueberry Yogurt Muffins are perfect for making ahead of time or enjoying straight out of the oven. Made with just 6 main ingredients, this dish is ready in just 30 minutes AND is gluten-free, low-carb, and keto-friendly!

There is nothing like a fresh batch of blueberry muffins. The smell alone is enough to make me swoon and the flavor brings me right back to my childhood. While muffins aren’t typically considered to be the healthiest breakfast, these Almond Flour Blueberry Yogurt Muffins will change your mind.

Unlike bakery-style blueberry muffins that are loaded with artificial sugars and wheat, these healthier muffins are the perfect alternative.

This recipe is low in carbs and sugar, making for the ultimate indulgence without any of the guilt. These blueberry muffins are soft, fluffy, and bursting with fresh and decadent flavors.

These Almond Flour Blueberry Muffins are ready in under 30 minutes, making them great for weekend meal prep. Made with wholesome ingredients like almond flour and Greek yogurt, they satisfy that blueberry muffin craving without the dreaded blood sugar spike.

Love making breakfast with yogurt? Don't miss these Peanut Butter and Jelly Yogurt Bowls.

Ingredients for almond flour blueberry muffins including almond flour, blueberries, eggs, yogurt, walnuts, and cinnamon.

What You’ll Need for Almond Flour Blueberry Muffins

To make these delicious almond flour blueberry yogurt muffins, you will need the following ingredients:

  • Almond flour: Almond flour is a wonderful flour alternative that is rich in vitamins, minerals, and healthy fats. It is also much lower in carbs than regular flour, not to mention it’s free of gluten.
  • Eggs: Eggs are jam-packed with protein, healthy fats, and tons of nutrients, including vital minerals like folate and iron.
  • Greek yogurt: Greek yogurt is different from other yogurts because it undergoes a straining process that removes the whey. It’s high in protein, yet lower in sugar than traditional yogurt. It also contains tons of essential vitamins and minerals.
  • Sweetener: Granular sweetener is a natural sugar replacement, however, it doesn’t have the bitter aftertaste commonly associated with other sugar replacements. It bakes and measures like regular sugar, making it perfect for this muffin recipe. Some keto-friendly brands to try are Swerve and Natvia.
  • Blueberries: Blueberries are as nutritious as they are sweet, not to mention they add beautiful color to our muffins.
  • Walnuts: One of the healthiest nuts on the planet, walnuts are loaded with healthy fats and protein. They also have a nutty flavor that pairs beautifully with these muffins. Almonds are work great in this recipe.

Recipe Tips for the Best Low Carb Blueberry Muffins

Here are a few tips for making these delicious and healthy muffins:

  • If you want to make muffins that overflow on top as they would in a bakery, try reducing the count to 10 muffins. You will want to use the same amount of batter, just make sure to fill the muffin liners generously.
  • For Instagram-worthy muffins, press some fresh blueberries into the tops of your muffins before baking them.
  • Make sure you give your muffins time to cool down. I know how tempting it can be to dive right into that warm and fluffy goodness, but the muffins will continue to firm as they cool, which helps to create the ideal consistency.
  • Never substitute almond flour for almond meal. They are not the same! Almond meal will give the muffins more of a grainy consistency, which you don’t want.
  • If you’re not a fan of almond flour, try swapping it out for coconut or oat flour.

Recipe Variations

One of the best parts about this recipe is how easy it is to customize! Here are some of my favorite ways to make it your own:

  • Switch up the fruit. Not a blueberry fan? No problem. You could make these muffins using another type of berry or fruit. Some of my top picks are raspberries, blackberries, and apples. 
  • Add some protein. For a more filling breakfast that also serves as a fantastic post-workout treat, try adding some extra protein. Options include vanilla protein powder, chia seeds, and flax seeds.
  • Swap out the nuts. This recipe would taste great with a variety of nuts, so don’t worry if you don’t love walnuts. You can swap out the walnuts for pecans, almonds, or even dark chocolate chips.

Low carb blueberry muffins with almond flour and walnuts stacked in a pile.

How to Store Almond Flour Blueberry Yogurt Muffins

A batch of these almond flour blueberry yogurt muffins is perfect for making ahead and have on-hand throughout the week. They’re super easy to reheat, making them the perfect grab-and-go breakfast for those mornings when you literally have to grab and go. To store, seal cooled muffins in an airtight storage container and store in one of two ways:

  • In the fridge for up to one week.
  • In the freezer for up to 4-6 months.

Pro tip: Never seal your muffins in a plastic bag or plastic wrap, as they will get soggy.

Absolutely! If that’s what you have available, you can absolutely use frozen blueberries in this muffin recipe. However, avoid thawing them first, as thawed blueberries will make your muffins soggy. I also recommend tossing them with a bit of almond flour first, which will help them to distribute more evenly throughout the batter.

The eggs act as a binder and help to give these muffins their structure. While I have not personally tried these muffins without eggs, you could try using mashed banana or a flax egg instead for a vegan-friendly swap. Keep in mind that substituting the eggs may alter the texture of the muffins.

Yes! Not only are these almond flour blueberry yogurt muffins keto-friendly, but they’re gluten-free as well. This is because we use almond flour instead of regular wheat flour. If you prefer another flour alternative, you can try using oat flour or coconut flour instead.

Coconut flour can not be substituted for almond flour in low-carb baking since they cook differently. Coconut flour absorbs more liquid than almond flour and the muffin will not turn out if made with coconut flour.

Almond Blueberry Muffin with Greek yogurt on a wooden cutting board and cut in half.
The Recipe
Almond flour yogurt blueberry muffins in a muffin tray with extra blueberries and walnuts on the side.

Almond Flour Blueberry Yogurt Muffins

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  • 2 1/2 cups almond flour
  • 1 tsp baking soda
  • 1/4 teaspoon salt
  • 1/2 cup granular sweetener
  • 3 eggs, beaten
  • 1 cup nonfat plain Greek yogurt (or full fat)
  • 1 tsp vanilla extract
  • 1 tsp cinnamon
  • 1 cup blueberries
  • 1/2 cup walnuts, chopped

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Preheat the oven to 400 degrees. Line a 12 hole muffin pan with liners and spray lightly with cooking spray.


In a large bowl, combine the almond flour, baking soda, salt, and granular sweetener. In another bowl, combine the eggs, yogurt, vanilla extract, and cinnamon. Add this into the almond flour mixture and stir until combined, making sure not to overmix. Gently fold in blueberries and walnuts.


Add the batter to the muffin pan, they should be almost full. Bake for 18-22 minutes until they are browned and a toothpick comes out clean.

Nutritional Facts
Serving Size: 1 muffin
Amount Per Serving
Calories 185
Calories from Fat 123
% Daily Value *
Total Fat 14g
Saturated Fat 1g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 47mg
Sodium 183mg
Total Carbohydrate 8g
Dietary Fiber 3g
Sugars 3g
Protein 9g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
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1 Comment
On Almond Flour Blueberry Yogurt Muffins
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February 9, 2024 - 10:02
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These were fantastic!!! Used the jumbo blueberries and I added a dab of Irish butter to the baked muffin and was so decadent!
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