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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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Video

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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Disclaimers

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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    Recipe Rating




  1. teacherlove says

    September 01, 2024 at 4:13 am

    These are good. I have tried them using different types of protein powder. I find that a casein-whey blend gives the best texture!!!

    Reply
    • Vered DeLeeuw says

      September 01, 2024 at 3:59 pm

      I'm glad you like these pancakes! Thank you for the comment and for sharing your findings.

  2. Rose says

    July 20, 2024 at 8:45 am

    3 stars
    These are a solid 3. For what they are, gluten-free, sugar-free, low carb, and high protein, they're not terrible, but they're not that good either.. I would hardly compare it to a delicious fluffy muffin. It is dense and eggy, And even spraying the muffin liners. They still stick, and are almost impossible to peel out of the muffin liner. Would be better off using parchment paper or maybe a silicone muffin pan.

    Reply
    • Vered DeLeeuw says

      July 20, 2024 at 10:20 am

      Thanks for the feedback, Rose. As stated in the recipe notes, it's best to use foil or parchment liners, as these muffins indeed stick to standard paper ones.

  3. Kaye Rowe says

    June 05, 2024 at 10:00 pm

    5 stars
    These muffins were excellent! I didn't have liquid stevia so just used dry and were yummy. I also loved that it only made 6 as these were just for me 🙂 Thank You for the recipe

    Reply
    • Vered DeLeeuw says

      June 06, 2024 at 9:33 am

      Glad you enjoyed these muffins, Kaye! Thank you for sharing your stevia tweak.

  4. Jasmine says

    April 04, 2024 at 5:47 pm

    5 stars
    Great recipe! Always on the hunt for protein recipes. I traditionally do protein muffins with banana base but have been on the hunt for one without and so happy to have found this one! Only thing I changed was using 1/4c Greek yogurt and 1/4c applesauce as I love baked goods like this on the moister side. I also use Lilys chocolate chips to keep it entirely (added) sugar free.
    I was able to make 9 muffins with this recipe. DELISH! Will definitely be keeping this recipe on hand to whip up as a protein snack often! Thank you for a great recipe.

    Reply
    • Vered DeLeeuw says

      April 04, 2024 at 6:43 pm

      You're very welcome, Jasmine! Thank you so much for the detailed review.

  5. Maralee says

    April 03, 2024 at 2:44 pm

    Could these be made with oat flour?

    Reply
    • Vered DeLeeuw says

      April 03, 2024 at 5:11 pm

      Hi Maralee,
      Oat flour can usually be substituted for almond flour at a 1:1 ratio. However, I only tested this recipe with almond flour.

  6. Julia says

    March 20, 2024 at 12:22 am

    5 stars
    I made these and used frozen raspberries instead of chocolate chips and regular sugar instead of stevia. They were good and even better when I had more straight out of the fridge - I liked the texture better cold which is unusual for me. Thank you!

    Reply
    • Vered DeLeeuw says

      March 20, 2024 at 9:54 am

      How interesting, Julia! Glad you liked them. Thank you for taking the time to review this recipe!

  7. Alice says

    February 28, 2024 at 6:02 pm

    5 stars
    I tried making these with standard white sugar as I wanted a high protein muffin but didn't want to use stevia since it's probably best to avoid it during pregnancy as it doesn't have as long a track record as sugar.

    They did turn a pretty golden brown on top as a result, but the batter seemed lighter and fluffier too - the chocolate all sunk to the bottom (I used half chips and half chopped chocolate). It also made 16 muffins instead of 12.

    They're still very tasty, they just don't look the nicest as the sinking effect has made the tops wrinkle as well. I'd think they are underdone, but the toothpick pulled out clean from the middle row of muffins when tested. Has anyone else who tried using white sugar experienced this? If not, perhaps it's my protein powder... I did use whey protein powder but not the brand that was linked. Perhaps that made a difference too.

    Reply
    • Vered DeLeeuw says

      February 28, 2024 at 10:25 pm

      Hi Alice,
      Thanks for sharing your experience! I don't think it's the sugar. It could be the protein powder. There are so many variables that it's difficult to predict the exact outcome. In any case, I'm glad you enjoy the flavor!
      By the way, dusting powdered sugar on top makes wrinkled baked goods look prettier. 🙂

  8. Emily says

    January 29, 2024 at 1:42 pm

    4 stars
    Just made these! I doubled the recipe because we are a family of four but followed the measurements and this yielded more than 12 muffins. It's probably closer to 16. I learned that "almost full" is a very subjective term haha so my muffins flooded the pan- I think 3/4 full max as these still rise. I think because mine were so full they did not cook properly and did in fact brown (a lot). If you plan on doubling the recipe like I did, I wouldn't put the full doubled amount of protein powder in there, unless you use flavorless because my vanilla flavored power really overwhelmed the muffins. It tasted like a birthday cake exploded in my mouth. But I bet my kids will go crazy for them!

    Reply
    • Vered DeLeeuw says

      January 29, 2024 at 2:16 pm

      Thank you for the detailed feedback, Emily! Very interesting.

  9. Catherine says

    January 21, 2024 at 8:45 am

    There are actually parchment cupcake liners now that work so so much better than the traditional foil or paper liners that I suggest you try. Baking keto foods for my mom I've learned that almond flour batters are the stickiest thing on the planet, these parchment liners come in clutch for this kind of cooking.

    happy baking~♡

    Reply
    • Vered DeLeeuw says

      January 21, 2024 at 9:14 am

      How interesting, Catherine. Thanks for the tip! I assume you mean something like these parchment cupcake liners. I'll give them a try!

  10. True self says

    July 16, 2023 at 4:51 am

    Would I need to change anything to make this a loaf instead of muffins? More liquid?

    Reply
    • Vered DeLeeuw says

      July 16, 2023 at 9:07 am

      I only tested this recipe in a muffin tin, so this is an educated guess. To make a loaf, you would need to double the recipe and, ideally, use a small loaf pan (8 X 4 inches).

      The baking time will increase. I suggest you start checking after 20 minutes. I don't think you would need to increase the liquid or make any other changes.

      If you decide to go ahead and try this recipe in a loaf pan, I would appreciate you coming back here and telling us about the results.

    • teacherlove says

      July 27, 2023 at 9:00 am

      5 stars
      Hello again.
      I did use the recipe as a loaf. I took your advice and doubled it. I baked it at 350°F for 30 minutes. It baked perfectly. Thank you. I have been needing something quick to grab on some mornings. This recipe works well as muffins or a loaf.

    • Vered DeLeeuw says

      July 27, 2023 at 2:05 pm

      Wonderful! Thank you so much for letting us know that this recipe works as a loaf.

    • Adela says

      January 18, 2024 at 6:42 pm

      can I switch to regular flour?

    • Vered DeLeeuw says

      January 18, 2024 at 7:05 pm

      Hi Adela,
      You can try using 1/2 cup of all-purpose flour instead of almond flour. If using all-purpose flour, you will likely need to increase the butter by two tablespoons and possibly add 1/4 cup of liquid such as milk. I only tested this recipe with almond flour, so this would be an experiment.

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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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