Curb your sweet tooth with these Homemade Chocolate Protein Muffins! Only 95 calories and 3 grams of protein each!
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I needed a food that would satisfy my sweet tooth, but not ruin my calorie intake or goals. These Chocolate Protein Muffins hit the spot.
They are chocolaty and sweet enough that you feel like you are eating dessert, but you don’t have to feel guilty about it.
Recipe Ingredient Notes
To make Chocolate Protein Muffins, you will need the following ingredients:
- Unsweetened cocoa powder
- Chocolate protein powder
- Whole wheat flour
- Sugar
- Baking powder
- Baking soda
- Eggs
- Milk
- Applesauce
- Vanilla extract
- Vegetable oil
- Mini chocolate chips
Equipment Needed
For this recipe, you only need a few simple kitchen tools. We recommend using the following equipment:



How to make Chocolate Protein Muffins
- Preheat oven to 400℉.
- Line muffin tins with cupcake liners or spray with nonstick cooking spray.
- In a large mixing bowl, combine cocoa powder, protein powder, whole wheat flour, sugar, baking powder and baking soda.
- Mix in eggs, milk, applesauce, vanilla and vegetable oil until well combined.
- Fill each cupcake liner ⅔ of the way full or use a large cookie scoop to place batter in cups.
- Sprinkle a few chocolate chips on top of each muffin before baking.
- Bake for 20 minutes or until set in the center.
Storage Suggestions
- Reheating: Preheat oven to 300°F. Reheat until warm for best results. Or microwave in 30 second increments for 1 to 2 minutes.
- Counter & Refrigerator: Place rolls in an airtight container or ziplock bag. Store in the refrigerator for 3 to 4 days. Store on the counter for 1-2 days.
- Freezer: Wrap each rolls individually in foils and place in an airtight freezer bag. Store in the freezer for 1 to 2 months.
Enjoy More Delicious Muffins
Whether bursting with fruit or studded with toasty nuts and chocolate chips, these muffin recipes will make it easy to start your day. Explore our comprehensive list of muffin recipes here.
- Baked Apple Fritter Muffins
- Cake Mix Blueberry Muffins
- Copycat Famous Dave’s Cornbread Muffins
- Mini Maple Pancake Muffins

Chocolate Protein Muffins Recipe
Curb your sweet tooth with these Homemade Chocolate Protein Muffins! Only 95 calories and 3 grams of protein each!
Serving Servings
Ingredients
- 6 Tablespoons unsweetened cocoa powder
- ½ cup chocolate protein powder
- 1 ½ cups whole wheat flour
- ½ cup sugar
- 1 teaspoon baking powder
- 1 ½ teaspoons baking soda
- 2 large eggs
- 1 cup milk
- 1½ cups unsweetened applesauce
- 1 Tablespoon vanilla extract
- 1 Tablespoon vegetable oil
- ½ cup mini chocolate chips
Instructions
- Preheat oven to 400℉.
- Line muffin tins with cupcake liners or spray with nonstick cooking spray.
- In a large mixing bowl, combine cocoa powder, protein powder, whole wheat flour, sugar, baking powder and baking soda.
- Mix in eggs, milk, applesauce, vanilla and vegetable oil until well combined.
- Fill each cupcake liner ⅔ of the way full or use a large cookie scoop to place batter in cups.
- Sprinkle a few chocolate chips on top of each muffin before baking.
- Bake for 20 minutes or until set in the center.
Notes
Feel free to add some walnuts for some extra texture.
Nutrition
Calories: 95 kcal · Carbohydrates: 16 g · Protein: 4 g · Fat: 3 g · Saturated Fat: 2 g · Polyunsaturated Fat: 1 g · Monounsaturated Fat: 1 g · Trans Fat: 1 g · Cholesterol: 18 mg · Sodium: 108 mg · Potassium: 94 mg · Fiber: 2 g · Sugar: 9 g · Vitamin A: 50 IU · Vitamin C: 1 mg · Calcium: 48 mg · Iron: 1 mg
Did You Make This Recipe?We’d love to hear your thoughts! Leave a review or a question in the comment section below the post.



















Just made these! They are fantastic. Added walnuts for some extra texture. Thank you so much!
Looking for recomwndation: chocolate protein powder.
Just made these, the taste is awesome. I used coconut milk and flour. I cooked the first batch and found them to be extremely dry so the 2nd batch I cooked I added a little veg oil, it helped but still a dry muffin. Will have to tweak the recipe because they taste great and the coconut flour and milk made it a great combo. Any suggestions for a moister muffin?
Ascent native whey protein
25g of protein and only 1 gram of sugar. Love this stuff
Zucchini really helps.
Is the nutrition information available?
The simple answer is add more liquid and egg(s), but I recommend looking up about coconut flour. It is different from grain flours and cannot be substituted without adaptations. Generally, use less flour, probably with another alternative flour and more eggs and liquid. I have a recipe for banana bread that uses only 1/2 c. of coconut flour, 3 TBL tapioca flour and 3 or 4 eggs and some other things. It’s delicious but I don’t know if I should plug someone else’s site on this one, so do a search and learn about coconut flour. It has good fiber and protein and is very filling. If it is ok to say, the website is called roasted root, but I learned about coconut flour from various websites.
I thought one of you used canned pumpkin with the kodiak pancake mix for muffins. I can’t find it.
Awsome muffins. Moist, not to sweet, low in calories and easy to make.
Such a good recipe! Since I used plant-based protein powder, I added just a bit extra of each wet ingredient (because I’ve heard that plant powder sucks up moisture in recipes). Turned out perfectly, so moist and delicious!
I followed all of the directions, but my muffins came out dry sticking to the cupcake liners. Is there anything you suggest to stop this? I’d love to try making them again.
Hi Katie – I’m so sorry that happened. How frustrating. There could be several culprits. 1. Packing the flour into the measuring cup 2. Over mixing the batter 3. Overbaking 4. Cooling the Muffins in the pan for too long even 5. Difference in elevation. I would try adding a little less flour next time or removing them from the oven a little sooner. Best of luck!
Fabulous. I tried them today. I used Orgain brand chocolate protein powder. I substituted Monk Fruit Sugar for the traditional sugar. I added 1 tsp Espresso powder. I agree with the previous reviewers. I cannot BELIEVE how good these are for how healthy they are. For me, it resulted in 14 regular sized muffins. This recipe is an awesome substitute for the chocolate needers among us. 🙂 Thank you for figuring it out and sharing!!!!