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Chocolate Protein Muffins

These soft and fluffy chocolate protein muffins are a bite of dessert in the morning to start your days on a sweet note. They’re sweetened with fruity coconut sugar, so that means more bites and no sugar-highs.

A stack of chocolate protein muffins with the baking tray in the background.

Easy Chocolate Protein Muffins

If you’re always looking for an excuse to have dessert for breakfast, these tender chocolate protein muffins are the perfect recipe for you. They’re loaded with gooey dark chocolate chips to keep the interior nice and moist. Coconut flour, sugar, and milk add nutty and creamy goodness. Best of all, they’re not packed with processed sugar and are easy to carry for a quick sweet bite.

Why You’ll Love These Chocolate Muffins

These simple chocolate protein muffins will turn into your favorite breakfast in no time.

  • Wholesome. There’s protein powder and chia seeds in the batter to keep you full all morning.
  • Great for on-the-go. Throw them into your bag on your way out for work. It doesn’t matter if they’re fresh or frozen.
  • Easy. This recipe is just like making box-mix muffins! Mix the wet and dry ingredients, then bake away.
  • Quick. 12 muffins in 30 minutes? It’s quicker than driving to your favorite bakery and back.
Chocolate protein muffins in the muffin tray.

What You’ll Need

Three types of plant-based flour help create the perfect fluffy texture for these chocolatey muffins. Scroll to the recipe card at the bottom of the post for exact quantities.

  • Almond flour – Use the kind that’s finely ground and has no bits of skin.
  • Tapioca flour – You can find it in the organic aisle at most grocery stores.
  • Coconut flour – Oat flour can be used as well.
  • Cocoa powder Make sure it’s unsweetened.
  • Chocolate protein powder Whey or pea protein both work.
  • Coconut sugar Dark brown sugar is a great substitute.
  • Chia seeds Feel free to use flax seeds.
  • Baking powder Always check the expiration date before adding it in.
  • Baking soda Avoid baking powder because it’ll give the muffins a metallic after-taste.
  • Egg – Don’t use plant-based alternatives.
  • Egg whites – You can use liquid egg whites.
  • Almond milk Oat or coconut milk can be used instead.
  • Coconut cream Full-fat is best.
  • Coconut oil Vegetable, corn, and canola oil work too.
  • Vanilla extract Feel free to leave it out.
  • Dark chocolate chips Use your favorite kind. Roughly chopped chocolate is a good swap.

How to Make Chocolate Protein Muffins

This healthy chocolate muffins recipe is as easy as your favorite box-mix. Scroll to the recipe card at the bottom of the post for more detailed instructions.

  • Prep the oven. Preheat the oven to 400F. Grease two muffin trays with nonstick spray and set them aside.
  • Combine the dry ingredients. Whisk the flours, cocoa powder, protein powder, coconut sugar, chia, baking powder, and baking soda in a large mixing bowl.
  • Combine the wet ingredients. Mix the egg, egg whites, almond milk, coconut cream, coconut oil, and vanilla extract in another mixing bowl until smooth.
  • Incorporate them. Pour the wet ingredients into the dry mixture and stir until just combined.
  • Add the chocolate chips. Gently fold in the chocolate chips.
  • Bake. Pour the batter into the muffin tray until each cavity is full 2/3 of the way. Pop the trays into the oven for 20 minutes or until a toothpick inserted in the center comes out clean.
  • Serve. Remove them from the oven and let them cool for at least 5 minutes. Serve and enjoy!
Muffins with a glass of milk and strawberries on the side.

Tips & Variation Ideas

Choosing the right liners makes a huge difference for these chocolate protein muffins (or any recipe) to make sure nothing sticks.

  • Use more add-ins. Stir 1/4-1/2 cup chopped nuts, dried cranberries, fresh cranberries, or shredded coconut into the batter for extra texture.
  • Swap the chips. Use milk, bitter-sweet, white, butterscotch, or peanut butter chips instead of dark chocolate chips.
  • Scoop it properly. Spoon the flour into your measuring cup little by little. Never scoop it all up at once. This leads to over-packing and causes you to add too much flour.
  • Use the right liners. Many muffin liners have a horrible sticking problem, so I prefer ones with nonstick coating. If you can’t find any, lightly grease your muffin tin (or regular liners) with nonstick baking spray.
  • Don’t over-mix. Only mix the batter until it’s just combined. Over-mixing leads to dense, rubbery muffins.
  • Add frosting. Spread peanut butter, almond butter, jam, or your favorite frosting on top for more of a dessert “feel”.
Halved muffin with a glass of milk on the side.

How to Store Chocolate Muffins

The muffins need to be fully cooled before you use any storage method.

  • Counter: Place them in an airtight container for up to 4 days. Keep them away from direct heat and sunlight.
  • Fridge: Store them in airtight containers or bags for up to 7 days. Place them far away from strong-smelling foods like onions to avoid the transfer of odors.
  • Freezer: Wrap each muffin in plastic wrap twice. Transfer them to freezer-friendly bags or containers. Freeze for up to 2 months. Thaw them overnight in the fridge or on the counter for 30-40 minutes.

More Muffin Recipes to Try

Halved muffin with a glass of milk on the side.

Chocolate Protein Muffins

This easy chocolate protein muffins recipe with chocolate chips is an indulgent breakfast option that won't give you a sugar-high.
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes
Servings: 12 muffins


  • Oven


  • ¾ cup almond flour
  • ½ cup tapioca flour
  • ¼ cup coconut flour
  • 6 tablespoons cocoa powder
  • ½ cup chocolate protein powder (2 scoops)
  • ½ cup coconut sugar
  • ¼ cup chia seeds
  • 1 teaspoon baking powder
  • 1 ½ teaspoons baking soda
  • 1 egg lightly beaten
  • 4 egg whites lightly beaten
  • 1 cup almond milk
  • 1 ½ cups coconut cream
  • 1 tablespoon coconut oil or vegetable oil
  • 1 teaspoon vanilla extract
  • 1 cup dark chocolate chips


  • Preheat the oven to 400°F. Liberally coat two standard muffin tins with non-stick spray and set aside, or line standard muffin tin with paper liners.
  • In a large mixing bowl, combine all dry ingredients.
  • In a small mixing bowl, combine all wet ingredients.
  • Create a well in the center of the dry ingredients. 
  • Pour the wet ingredients into the well and begin to mix. 
  • Add the chocolate chips right before the mixture is fully combined. Do not over mix, just blend the chips into the batter. 
  • Pour batter evenly among the muffin cups and bake for approximately 20 minutes.
Course: Breakfast, Breakfast/Brunch, Dessert, Snack
Cuisine: American


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