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Home » Recipes » Muffins

Amazing Keto Chocolate Protein Muffins with Coconut Flour

Published: Mar 20, 2021 · Last Modified: Feb 21, 2025 by Haylee Jane Monteiro · This post may contain affiliate links

The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

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The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

I feel like I say this every time, but another SUCH a perfectly soft and moist muffin right here!

After loving the vanilla coconut flour protein muffins I made a few weeks ago, I had to create a chocolate version too. Quite a small adaptation so just as easy.

Another beautiful nutrition label here as well with more protein than total carbs; And with most of those being fiber, the net carbs on these chocolate muffins are, wait for it, 2.7g only! 

Ohhhh! Now I’m considering making a savory version of coconut flour muffins and having them for a low carb dinner.

The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

Ingredients for Keto Chocolate Protein Muffins

These coconut flour chocolate protein powder muffins are made with a few clean and healthy ingredients, making them the ideal sugar free, gluten free, low carb, keto and high protein muffins!

  • Coconut flour
  • Chocolate Protein Powder – I use quest nutrition chocolate for these protein powder muffins for a sugar free and keto protein muffin recipe since (since it’s sweetened with stevia).
  • Unsweetened Cocoa Powder or Cacao Powder
  • Almond Milk to add moisture to the muffins – the protein powder and coconut flour both absorb a lot.
    You can use normal milk, but almond milk gives a dairy free recipe.
  • A bit of Creamy Peanut Butter
  • Eggs – a lot of these since this is a coconut flour baked good.
  • Baking Powder

Are Muffins High in Carbs?

Most regular store bought muffins are high in carbs because they use all purpose flour, or tor other regular flour alternatives. Since these keto protein muffins are made with coconut flour, they have a total of 8.1g carbs, of which 5.4g is fiber – so all you have is 2.7g of net carbs!

So if you’re ever looking for low carb muffin recipes with protein powder, you need to try this ketp chocolate protein muffin!

The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

How to make Chocolate Protein Powder Muffins with Coconut Flour

These easy chocolate protein muffins are actually really simple to make, especially because you don’t need to worry about over-mixing the batter.

  1. Preheat your oven to 350°F and line 9 cups of a muffin tin with cupcake lines. Lightly spray the insides with oil spray (so the muffins come off easily)
    You can also use a non-stick pan.
  1. Whisk the eggs, milk, peanut butter and vanilla in a large bowl.
  1. Add the dry ingredients: coconut flour, chocolate protein powder, cacao powder or cocoa powder and baking powder and whisk. You should have a thick muffin batter;
    Let it rest a bit so the coconut flour has time to absorb the moisture.
  1. Divide the mix among the muffin cups, filling them about ¾ way to the top.
    Optionally, top with dried nuts/seeds or sugar free chocolate chips.
  1. Bake the muffins for about 23 minutes until a tester inserted into the center comes out dry.
The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

How to store Coconut Flour Chocolate Protein Muffins

Chocolate protein powder muffins can be stored on the countertop, in the fridge or the freezer for an healthy keto breakfast or dessert.

Keep the keto chocolate protein muffins in an airtight container on the countertop for up to 3 days or fridge for 6 days.

To freeze, wrap individual chocolate protein powder coconut flour muffins in plastic wrap, place in a freezer-safe zipper bag, and freeze up to 3 months. Leave them on the countertop or place them in the fridge overnight to thaw. I would not recommend using the microwave.

Tips for perfect High Protein Low Carb Muffins Recipe

This low carb muffin recipe with protein powder, although easy, can be a bit tricky if you don’t get all the steps right. This is especially because coconut flour and protein powder are both really absorbent. Here’s some tips to get it right:

  • Use room temperature eggs and room temperature milk; This is so the wet ingredients and dry ingredients can mix well.
  • Use runny, creamy peanut butter, room temperature again, so it mixes well with the batter.
  • A whey-caesin chocolate protein protein powder works best for these keto coconut flour muffins, so I really recommend making them with quest protein powder.
  • Taste the batter and see if you need some extra sweetener. I’d recommend using stevia powder to maintain the consistency of the batter and have keto protein muffins.
  • Lightly grease the cupcake liners or muffin pan with cooking spray – this will allow the chocolate coconut flour muffins to come off easily!

Upgrade your Easy Chocolate Protein Powder Muffins

This recipe makes just basic coconut flour chocolate protein muffins, but there’s plenty of options for mix-ins and toppings you could add.

Mix in some nuts, seeds or chocolate chips into the protein coconut flour muffins batter.

Make sure to use low carb ones to keep these muffins suitable for the keto diet.

Another option is to just add them on top of the muffins and then bake.

For the chocolate chips, I recommend the sugar free ones from Lakanto (you get a discount with the code HAYLSKITCHEN).

More Coconut Flour Protein Powder Recipes to try:

  • Black Bean Protein Brownie Batter
  • Chickpea Cookie Dough Protein Balls – Simple & Healthy!
  • Protein Chickpea Cookie Dough (Low Calorie & Sugar Free)
  • Soft Low-Fat No-bake Peanut Butter Protein Cookies

More Keto Coconut Flour Recipes to try:

  • Keto & Low Carb Coconut Flour Bread
  • Light, Fluffy Coconut Flour Pancakes (Keto & Low Carb)
  • Dark Chocolate Coconut-Spaghetti Squash Cake

More Quest Protein Powder Muffins:

  • Oil Free Apple Protein Muffins (Whole Wheat)
  • Chocolate Banana Protein Muffins
  • Coconut Flour Protein Muffins

Amazing Keto Chocolate Protein Muffins with Coconut Flour

5 from 1 vote
Print recipe Pin Recipe
Prep Time5 minutes mins
Cook Time23 minutes mins
Total Time28 minutes mins
Servings: 9 muffins
Calories: 121kcal
Course: Breakfast, Dessert, Post-Workout
Cuisine: American
The most amazing Keto Chocolate Protein Muffins made with coconut flour and sweetened with protein powder. With 2.7g net carbs, these easy chocolate protein powder muffins are the perfect low carb high protein muffin recipe!

Ingredients

  • ⅔ cup Coconut Flour, 74g
  • ½ cup Chocolate Protein Powder, 45g, 1½ scoops
  • ⅓ cup Unsweetened Cocoa Powder, Cacao Powder
  • 3 teaspoon Baking Powder
  • 1 cup Almond Milk, or other at room temperature
  • 4 Eggs, room temperature, or liquid egg substitute
  • 2 tablespoon Creamy Peanut Butter, 32g
  • 1 teaspoon Vanilla Extract
  • Optional toppings: 1-2 tablespoon Dried Fruit, Chocolate Chips, Nuts or Seeds

Instructions

  • Preheat oven to 350°F, line 9 cups of a muffin pan with cupcake liners, and lightly spray insides with cooking spray (or use non-stick pan).
  • In a large bowl, whisk together milk, eggs, peanut butter and vanilla.
  • Add in coconut flour, chocolate protein powder, cocoa powder and baking powder, and whisk to combine.
  • Batter should be fairly thick; Add 1-2 tablespoon water if it’s too thick, or 1 tablespoon more coconut flour if it’s too runny.
  • Divide the batter among muffin cups, about ¾ way to the top. Sprinkle optional toppings.
  • Bake for 23-25 minutes. A toothpick inserted into center comes out dry.
  • Cool for 5 minutes, then remove from pan. Transfer to a wire rack to cool completely, about 10 minutes, and enjoy.

Notes

Recipe adapted from my Coconut Flour Protein Muffins.
  • Taste the batter and see if you need some extra sweetener; I’d recommend stevia if needed.
  • Nutrition value is calculated using products recommended below.
Storage:
  • Let the muffins cool completely before storing so they remain fresh.
  • Room temperature: 2-3 days, tightly wrapped in plastic wrap or airtight container.
  • Fridge: 1 week in an airtight container.
  • Freezer: 3 months, wrapped in plastic wrap and then placed in freezer bags.
Product Recommendation:
  • Quest Nutrition Chocolate Milkshake Protein Powder
Nutrition:
  • Servings: 9 muffins | Serving size: 1
  • Calories: 121kcal
  • Fat: 6.3g | Saturated fat: 2.6g
  • Carbohydrates: 8.1g | Fiber: 5.4g | Sugar: 1.5g
  • Protein: 9.1g

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Comments

  1. Haylee Jane Monteiro says

    May 15, 2025 at 11:46 pm

    Hi Mary so glad you tried the recipe and liked it so much! Haha I know right, the muffin pans are indeed a pain to clean

    Reply
  2. Mary Mahoney says

    April 10, 2025 at 7:25 am

    5 stars
    I had some coconut flour to use, and found this recipe – am I glad I found it! I only had vanilla protein powder, but they still taste very chocolate with the added chocolate powder. I also used almond butter instead of peanut butter.
    I detest cleaning muffin pans, so I just baked them in a brownie pan and they are outstanding.

    Reply

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Hi, I'm Haylee!

I use my passion for baking (and my sweet tooth) to create healthy, high protein, low fat and sugar free desserts and sweet treats that are actually delicious.

Come join me in Hayl's Kitchen and let's eat high protein, sweet and guilt free!

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