Chocolate Protein Muffins – Chocolate Protein Muffins are filled with chocolatey goodness and maintain the perfect balance of salty and sweet. They are easy to make for meal prep and breakfast on the go. Plus, they’re loaded with protein and healthy fat to keep you satiated throughout the day!

WHAT YOU NEED TO MAKE THIS RECIPE
- Almond Flour: For best results, use blanched almond flour. Blanched almonds are almonds with their skins removed, making them perfect for muffins.
- Chocolate Protein Powder: I use chocolate protein powder to flavor the muffins; you can also use unsweetened cocoa powder if you prefer.
- Sweetener: I use monk fruit for a few reasons. We always have it in our pantry, and it is the only sweetener that doesn’t leave a strange after-taste.
- Baking Powder: To ensure the muffins don’t become too dense, use baking powder.
- Salt: Salt offsets the sweetness.
- Butter: Melted butter pairs with the almond flour, which will dry out baked goods otherwise.
- Almond Milk: Adding to the nuttiness of the pancakes, almond milk provides needed moisture, and thins out the batter.
- Eggs: Eggs provide structure and added protein.
- Vanilla Extract: Vanilla extract is perfect for a bit of sweetness.
- Chocolate Chips: Lily’s sugar-free chocolate chips or cacao nibs work best for these muffins.
HOW TO MAKE CHOCOLATE PROTEIN MUFFINS
The full recipe with measurements is in the recipe card below.
Preheat the oven to 350° F (176° C) and line a muffin tin or pan with liners. Then, combine the dry ingredients in a mixing bowl.

In a separate mixing bowl, add the wet ingredients: melted butter, beaten eggs, vanilla, and almond milk- one by one. Careful not to over-mix.
Add the wet ingredients to the bowl with the dry ingredients, then fold in the chocolate chips.

The batter will be thick and dense, so use a spoon to divide the batter evenly among the prepared muffin liners ¾ of the way. Top each one with a few more chocolate chips.

Bake for 20-25 minutes.

Retrieve the muffins from the oven and immediately remove the muffins from the tin using a fork. Let the muffins cool before serving them.

EXPERT TIPS
- If storing your almond flour in the fridge, remember to bring almond flour to room temperature before baking. Cold almond flour absorbs more of the liquid, resulting in a more dense batter and dried-out muffins.
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SERVING SUGGESTIONS
If you feel like changing things up a bit, here are some ingredients to consider adding to the muffins.
- Chopped Pecans or Walnuts
- Chia Seeds or Flax Seeds
- Unsweetened Coconut Flakes
- Fresh Raspberries
- Peanut Butter
- Salted Caramel Chocolate Chips
WHAT TO DO WITH THE LEFTOVERS
- Refrigerate – Add the leftover muffins to a reusable bag or container and leave them on the counter until you’re ready to eat.
- Freeze – Allow the muffins to cool. Then add them to a freezer-safe container or bag. Chocolate protein muffins freeze for two months, but I doubt you can wait that long.
- Thaw – Set them onto the counter to defrost when you’re ready to eat.
- Reheat – Warm them in the microwave for 10-15 seconds.
FREQUENTLY ASKED QUESTIONS
How do I keep the muffins from falling apart?
1. Don’t over mix the batter.
2. Remove the muffin liners from the tin or pan immediately after baking. I set them onto a wire rack to cool once I pull them.
3. Only fill the muffin liner ¾ full.
Can children eat protein muffins?
Our children love these muffins for breakfast, and since they are packed with protein, it only takes a little bit to keep them full at school. Plus, chocolate is the perfect way to sneak eggs into a toddlers diet.
MORE BREAKFAST AND SNACK RECIPES:
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Chocolate Protein Muffins
Equipment
Ingredients
- 2 cups almond flour, blanched
- ¾ cup chocolate protein powder
- ½ cup monk fruit sweetener
- 2 teaspoons baking powder
- ¼ teaspoon salt
- ½ cup butter, melted
- ¼ cup almond milk, unsweetened
- 3 large eggs, beaten
- 1 teaspoon vanilla extract
- ¾ cup sugar-free chocolate chips
Instructions
- Preheat the oven to 350° F (176° C) and line a muffin tin or pan with liners. Then, combine the dry ingredients in a mixing bowl.
- In a separate mixing bowl, add the wet ingredients: melted butter, beaten eggs, vanilla, and almond milk- one by one. Careful not to over-mix.
- Add the wet ingredients to the bowl with the dry ingredients, then fold in the chocolate chips.
- The batter will be thick and dense, so use a spoon to divide the batter evenly among the prepared muffin liners ¾ of the way. Top each one with a few more chocolate chips. Bake for 20-25 minutes.
- Retrieve the muffins from the oven and immediately remove the muffins from the tin using a fork. Allow the muffins time to cool before serving them.
Notes
- If storing your almond flour in the fridge, remember to bring almond flour to room temperature before baking. Cold almond flour absorbs more of the liquid, resulting in a more dense batter and dried-out muffins.
- The nutritional information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for professional advice.
RJ
Wednesday 8th of June 2022
These were fantastic. So easy the kids made it with me. So flavorful that you don't even realize that they are low-carb/sugarfree.
Tressa Jamil
Sunday 12th of June 2022
I love that you baked these with your kiddos. That's a favorite pastime of ours too.