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Home » Recipes » Muffins

Double Chocolate Protein Muffins

Modified: Jun 12, 2025 · Published: Mar 20, 2025 by Morgan Peaceman · This post may contain affiliate links · Leave a Comment
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Double chocolate protein muffins are the ultimate snack hack-sweet enough to feel like a treat but packed with plenty of protein to keep you full and satisfied.

They're fluffy AF, chocolatey, and perfect for a post-gym bite or a grab-and-go breakfast. Basically, it's like having dessert for breakfast, and I'm not mad at it.

Six chocolate protein muffins in a porcelain basket with chocolate chips surrounding.

Studded with a ridiculous amount of chocolate chips, and clocking in at around 10 grams of protein per muffin (depending on the brand of greek yogurt used), these muffins will quickly become part of you meal prep rotation.

Jump to:
  • Recipe at a Glance
  • Trusty Tips and Key Reminders
  • Important Ingredients
  • Step by Step Process Photos
  • Frequently Asked Questions
  • Hungry for More?
  • Double Chocolate Protein Muffins

Recipe at a Glance

  • Bake Level: Easy, easy, easy. You won't believe how approachable this recipe is. One bowl is all it takes from start to finish.
  • Baking Time: These muffins bake for 22-23 minutes, with the batter coming together in just 10. The entire recipe takes just about 30 minutes, leaving you tons of time to do a million and five other things while they bake.
  • Taste: I'll be honest, the first time I tried these after my first bake, they tasted a little, um, healthy. After making them a few times and adjusting as necessary, the final taste is fluffy, chocolatey (without overpowering), and definitely on the more filling side (thanks to the protein in them).
  • Pair With: Make this protein muffins along with protein pancakes like my cinnamon banana protein pancakes, or my paleo-style pancakes. You could also whip up a hearty batch of my blender oatmeal pancakes for a well-rounded (and balanced) brekkie.

Trusty Tips and Key Reminders

  1. Do not over-mix - We've talked about this in a few of my recipes but it's so worth repeating. DO NOT OVER MIX THE BATTER! Switch to a spatula when folding in the choco chippies and the flour. This eliminates overworking the gluten in the flour, thus causing the muffins to become chewy, gummy, and yucky.
  2. Use a cookie scoop - If you're anything like me, you had to make a very large mess in the kitchen. To alleviate this, add the batter to the muffin tin using a cookie scoop. Much more precise too.
  3. Rotate the pans - Rotating the pans halfway through the muffins baking helps the muffins to bake evenly and prevent burning. In my first test, I left them alone and the ones in the back burned. It wasn't cute.
  4. Coat the Chocolate - Toss the chocolate chips in a bowl with just a little flour to prevent them from sinking to the bottom of the tin.
Ingredients for double chocolate protein muffins.

Important Ingredients

  1. Cocoa Powder - Cocoa powder aids in making these muffins super chocolately and decadent. We don't use a WHOLE lot of it as these muffins aren't meant to be overpowering.
  2. Protein Powder - I love using Ancient Nutrition Multi-Collagen Protein Powder in muffins because it helps my joints, hair, skin, nails, and gut. Plus, you literally do not taste it.
  3. All Purpose Flour - I love using traditional all purpose flour for these muffins as it always yields a consistent texture. You can always swap out the all purpose and use 1:1 gluten free flour.
  4. Baking Salt - Baking salt helps to balance out the sweetness in all of the other ingredients.
  5. Eggs - Eggs are essential in making baked goods such as muffins. I would recommend taking them out of the fridge so they are room temperature when mixing them. Plus, eggs also add to the protein.
  6. Sugar - Traditional granulated or cane sugar is the go to choice for making these as it's a very standard ingredient in baked goods.
  7. Oil - I prefer to use an avocado oil in my baking as it's neutral, smooth, and has a lot of nutritional benefits. If you want to use olive oil you can too, or even canola oil.
  8. Vanilla Extract - Vanilla extract is important to help bring out other flavors of the ingredients.
  9. Greek Yogurt - Another big factor in making these muffins higher in protein. I prefer to use whole fat yogurt and some of my favorites are from Trader Joe's (the Thick and Creamy or European one) Maia (it's a grass fed one with 20g of protein in just one cup), or Chobani whole fat.
  10. Chocolate Chips - Of course, you can't have chocolate muffins without chocolate chips!

Be sure to check out the recipe card at the end of this post for more information about quantities, measurements, and specific cooking instructions.

The inside of a chocolate protein muffin with chocolate chips.

Step by Step Process Photos

Wet ingredients such as eggs, sugar, vanilla extract, greek yogurt, and oil mixed together in a bowl.

Step 1: Preheat the oven to 375º and line a muffin tin with liners.

In a large mixing bowl, crack in the eggs and whisk together with the sugar until fully combined and smooth. Pour in the oil, vanilla extract, and add in the greek yogurt. Whisk until the batter comes together, then stop!

Cocoa powder added to a bowl of wet muffin ingredients.

Step 2: To the bowl, add in the cocoa powder, and fold in with a spatula.

Dry ingredients like baking powder, baking soda, baking salt, flour, and protein powder added to a bowl of wet muffin ingredients.

Step 3: Pour the flour, baking powder, baking soda, baking salt, and protein powder, then gently fold together with a rubber spatula until just combined, then stop.

A picture of a muffin tin filled with three unbaked muffins with chocolate chips on top.

Step 4: Using a large cookie scoop, take one large scoop of batter and add to each of the muffin liners. Top off with extra batter until all the remaining batter is used.

Add a sprinkle of additional chocolate chips on top, then bake for 23 minutes.

Close up of the top of a chocolate protein muffin.

Frequently Asked Questions

How do I store the leftover muffins?

Place any leftover muffins in an airtight container and store on the countertop for up to 4-5 days.

If you'd like to throw some in the freezer, you can do so by adding the remaining muffins to a large plastic food storage bag for up to two months.

What if I don't have greek yogurt?

You can use regular yogurt but it may not have as much protein and could also yield a different taste and texture.

Can I swap the flour in these muffins?

Yes! Use a trusty 1:1 gluten free flour like Bob's Red Mill or Primal Palate.

Which type of protein powder do you recommend I use?

Such a great question! I really do like using Ancient Nutrition's protein powders, as they have a wide variety of flavors and types such as plant based, whey, bone broth, and collagen!

Other brands I recommend include Orgain or Thrive Market's brand.

Can I make these into mini muffins, or into an entire loaf?

Yes! You make these muffins into an entire loaf or bite size, but you will need to adjust the time.

For Minis: Bake for 16ish minutes (check for doneness)

For Loaf: bake for 55m to 1 hour.

Close up of Six chocolate protein muffins in a porcelain basket with chocolate chips surrounding.

Hungry for More?

Check out these other higher protein recipes to keep you achieving your protein goals!

  • High protein ground beef taco bowl over rice with a lime.
    High Protein Ground Beef Taco Bowl
  • taco zucchini boat
    Easy Healthy Taco Stuffed Zucchini Boats Recipe
  • Fluffy Almond Butter Collagen Muffins 
  • Healthy and Creamy Tomato Basil Pasta Sauce Recipe

Did you love this recipe? ⭐️⭐️⭐️⭐️⭐️ If you're just as in love with this recipe as I am, please share a comment below and rate it! Better yet, share this recipe with family and friends!! Thank you!

Six chocolate protein muffins in a porcelain basket with chocolate chips surrounding.

Double Chocolate Protein Muffins

Morgan Peaceman
Ramp up your protein intake with these ultra moist and fluffy chocolate protein muffins made with protein powder and greek yogurt.
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 22 minutes mins
Total Time 32 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 12 servings
Calories 399 kcal

Equipment

  • large mixing bowl
  • Muffin tin and liners
  • Cookie scoop
  • spatula
  • whisk

Ingredients
  

  • 256 grams All Purpose Flour 2 cups
  • 1 teaspoon Baking powder
  • ½ teaspoon Baking Soda
  • ¼ teaspoon Baking Salt
  • 4 scoops Protein Powder I prefer Ancient Nutrition
  • 2 large Eggs room temperature
  • 200 grams Cane or Granulated Sugar 1 cup
  • 1 tablespoon Vanilla Extract
  • ¾ cup Avocado Oil
  • ¾ cup Greek Yogurt whole fat; room temperature
  • 1 cup Chocolate Chips

Instructions
 

  • Preheat the oven to 375º and line a muffin tin with liners.
  • In a large mixing bowl, crack in the eggs and whisk together with the sugar until fully combined and smooth. Pour in the oil, vanilla extract, and add in the greek yogurt. Whisk until the batter comes together, then stop!
  • To the bowl, add in the cocoa powder, and fold in with a spatula.
  • Pour the flour, baking powder, baking soda, baking salt, and protein powder, then gently fold together with a rubber spatula until just combined, then stop.
  • Using a large cookie scoop, take one large scoop of batter and add to each of the muffin liners. Top off with extra batter until all the remaining batter is used.
  • Add a sprinkle of additional chocolate chips on top, then bake for 23 minutes.

Notes

We've talked about this in a few of my recipes but it's so worth repeating. DO NOT OVER MIX THE BATTER! Switch to a spatula when folding in the choco chippies and the flour. This eliminates overworking the gluten in the flour, thus causing the muffins to become chewy, gummy, and yucky.

Nutrition

Calories: 399kcalCarbohydrates: 45gProtein: 10gFat: 20gSaturated Fat: 5gPolyunsaturated Fat: 2gMonounsaturated Fat: 10gTrans Fat: 0.004gCholesterol: 52mgSodium: 172mgPotassium: 138mgFiber: 1gSugar: 26gVitamin A: 46IUCalcium: 104mgIron: 1mg
Tried this recipe?Let us know how it was!

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Hey, I'm Morgan

I'm a huge foodie and it is my mission to make mealtime way less hectic. On this site you'll find easy and accessible family friendly recipes that are perfect for weeknights, weekends, and meal prep!

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