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Home » Breakfast Recipes » Protein Muffins

Protein Muffins

A photo of Vered DeLeeuw.
by Vered DeLeeuwUpdated Jun 22, 2025
26 Comments
4.92 from 35 votes

Jump to Recipe Review Recipe

These easy-to-make, fluffy protein muffins are made with almond flour and protein powder. A handful of chocolate chips and vanilla extract add amazing flavor.

Protein muffins are served on a wooden board.

These protein muffins are so delicious! They are light and fluffy, and each of them contains 13 grams of protein. I love how filling they are. When I have two of them for breakfast, I'm not hungry for hours. Two other high-protein breakfast options are chaffles (36 grams of protein per serving) and protein pancakes (31 grams of protein per serving).

Ingredients and Variations

The ingredients needed to bake protein muffins.

See the recipe card for exact measurements. Here are my comments on some of the ingredients.

  • Greek yogurt: Whole-milk yogurt has the best flavor. Sour cream works, too, but has less protein.
  • Sweetener: I use stevia. You can use a granulated sweetener instead.
  • Vanilla extract: It's fun to use different flavor extracts instead of vanilla. My favorite is coconut extract.
  • Butter: You can use oil instead of butter. I generally prefer the flavor of butter in these muffins, but macadamia nut oil is delicious! You can also use a neutral oil such as avocado oil.
  • Almond flour: I use superfine almond flour. I don't recommend using a coarse almond meal in this recipe.
  • Whey protein powder: I use Biochem unflavored protein powder.
  • Dark chocolate chips: I use 85% cacao chocolate chips by Pascha.

Instructions

The detailed instructions and step-by-step photos are included in the recipe card. Here's a quick overview.

In a large bowl, whisk the eggs, Greek yogurt, melted butter, stevia, and vanilla. Mix in the almond flour, followed by the protein powder and baking powder. Whisk until smooth.

A smooth batter in a mixing bowl.

Fold in the chocolate chips, reserving 24 to sprinkle on the muffins. Spoon the batter into foil-lined muffin cups. Top each muffin with 4 chocolate chips.

Topping the muffins with chocolate chips.

Bake the muffins in a preheated 350°F oven until a toothpick inserted in one of the muffins comes out clean, 17-19 minutes. Cool the muffins in the pan for 5 minutes and for 10 more minutes on a cooling rack before serving.

A hand holding a bitten muffin.

Recipe Tips

  1. Sometimes, I add a teaspoon of orange or lemon zest. It greatly enhances the muffins' flavor.
  2. Foil or parchment liners work best in this recipe to prevent sticking. These muffins stick to standard paper liners. If using standard paper liners, remove them while the muffins are still warm to minimize sticking. 
  3. The muffins will not brown much, even when they are ready, so please go by the dry toothpick test and not by their color. They are ready when a toothpick inserted in their center comes out clean.
  4. Protein powder is very drying, so it's best to measure it by weight, as you see me doing in the photo below, and not by volume.
Weighing protein powder.

Recipe FAQs

Is this a make-ahead recipe?

The muffins keep reasonably well in the fridge or freezer, but their texture is best when freshly baked. You can mix the batter the night before, pour it into the muffin pan, cover it with cling wrap, and refrigerate it, then bake the muffins in the morning.

Make ahead muffin tin wrapped in plastic wrap.

Can I use coconut flour instead of almond flour?

No. The two flours are very different. Coconut flour is very absorbent and has a drying effect on baked goods. It won't work in this recipe.

Can I add blueberries instead of chocolate chips?

Yes, but blueberries are heavier than chocolate chips and can sink to the bottom, as shown in the image below. This often happens when the batter is thin, as is the case here.

Protein muffins with blueberries.

How long can I keep the leftovers?

These muffins keep fairly well in the fridge, in an airtight container (as shown in the photo below), for 4-5 days and can be gently warmed up in the microwave. If you made them with blueberries, place them on paper towels to absorb extra liquid. These muffins also freeze well in freezer bags. You can thaw them in the microwave.

Storing protein muffins in a glass food storage container.

Serving Suggestions

These protein muffins are perfect for breakfast. I like to have one or two of them with my morning coffee, as shown in the photo below.

A protein muffin is served with coffee.

They're also excellent as an afternoon snack. I often pair one of them with a glass of almond milk for a delightful afternoon pick-me-up.

Recipe Card

Protein muffins are served on a wooden surface.
4.92 from 35 votes
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Fluffy Protein Muffins

These fluffy protein muffins are made with almond flour and protein powder. They contain 13 grams of protein per muffin!
Prep Time15 minutes mins
Cook Time20 minutes mins
Rest time15 minutes mins
Total Time50 minutes mins
Course: Breakfast
Cuisine: American
Diet: Gluten Free
Servings: 6 protein muffins
Calories: 226kcal
Author: Vered DeLeeuw
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Ingredients

  • Avocado oil spray - for the muffin liners
  • 2 large eggs
  • ½ cup Greek yogurt - plain, whole milk
  • ¼ cup butter - unsalted, melted, and slightly cooled
  • 1 teaspoon stevia glycerite - equals about ⅓ cup of sugar
  • 1 teaspoon pure vanilla extract
  • ½ cup superfine almond flour - 2 ounces
  • 2 scoops whey protein powder - unsweetened; 46 grams
  • 1 teaspoon baking powder - gluten-free if needed
  • ⅓ cup dark chocolate chips - divided; 2 ounces

Instructions

  • Preheat the oven to 350°F. Line a 6-cup muffin tin with liners and lightly spray them with oil. Foil liners work best.
    Muffin pan with foil liners.
  • In a large bowl, whisk the eggs, Greek yogurt, melted butter, stevia, and vanilla.
    The liquid ingredients in a mixing bowl.
  • Mix in the almond flour, followed by the protein powder, and finally, the baking powder. Mix until smooth.
    A smooth batter in a mixing bowl.
  • Fold in the chocolate chips, reserving 24 chocolate chips to sprinkle on the muffins.
    Adding chocolate chips to the batter.
  • Spoon the batter into the prepared muffin cups, filling them almost full. Top each muffin with 4 chocolate chips.
    Topping the muffins with chocolate chips.
  • Bake until a toothpick inserted in one of the muffins comes out clean, 17-19 minutes. They will not brown much.
  • Cool the muffins for 5 minutes in the pan on a wire rack and then for 10 more minutes directly on the rack before serving.
    A hand holding a bitten muffin.

Notes

  • Foil or parchment liners work best in this recipe to prevent sticking. These muffins stick to standard paper liners. If using standard paper liners, remove them while the muffins are still warm to minimize sticking. 
  • Protein powder is very drying, so it's best to measure it by weight using a kitchen scale, not by volume. 
  • You can mix the batter the night before, pour it into the muffin pan, cover it with cling wrap, and refrigerate it. Then, bake the muffins in the morning.
  • You can replace the chocolate chips with ½ cup of blueberries. The blueberries tend to sink to the bottom of the muffins, but the muffins are still delicious. Coating the blueberries in a teaspoon of cornstarch before adding them to the batter helps mitigate some of the sinking, but doesn't prevent it. 
  • You can double this recipe and bake 12 muffins. They keep fairly well in the fridge, in an airtight container, for 4-5 days and can be gently warmed up in the microwave. If you made them with blueberries, place them on paper towels to absorb extra liquid. These muffins also freeze well in freezer bags. You can thaw them in the microwave.

Nutrition per Serving

Serving: 1 muffin | Calories: 226 kcal | Carbohydrates: 5 g | Protein: 13 g | Fat: 16 g | Saturated Fat: 8 g | Sodium: 128 mg | Fiber: 1 g | Sugar: 2 g

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Most recipes are low-carb and gluten-free, but some are not. Recommended and linked products are not guaranteed to be gluten-free. Nutrition info is approximate. Please verify it independently. The carb count excludes non-nutritive sweeteners. Please read these Terms of Use before using any of my recipes.

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Comments

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  1. Mariana says

    February 19, 2025 at 3:22 pm

    Could I use vegan protein instead of whey?

    Reply
    • Vered DeLeeuw says

      February 19, 2025 at 7:05 pm

      Hi Mariana,
      I'm not sure. I only tested this recipe with whey protein powder. Another commenter recently said, "These are good. I have tried them using different types of protein powder. I find that a casein-whey blend gives the best texture."

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Healthy Recipes Blog was founded in 2011 by Vered DeLeeuw. It features real food recipes with a focus on low-carb and gluten-free ingredients. All recipes are nutritionally reviewed by a Registered Dietitian. Contact us at HealthyRecipesBlog@gmail.com.

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