Healthy Chocolate Brownie Muffins (Almond Flour, High Protein)
Oh, goodness! These Healthy Chocolate Brownie Muffins (Almond Flour, High Protein) are so fudgy that they are basically brownies without any refined sugar. Only healthy ingredients, lots of protein, and natural sweeteners.

Healthy Chocolate Muffins with Almond Flour
This recipe marks one of my proudest moments. I developed it from scratch–literally. Yep, this recipe for healthy almond flour chocolate muffins is an original one.
Years ago, I used to make a “healthy” chocolate banana bread that…um…in fact included half a cup of brown sugar. Needless to say, refined sugar does not fit under the umbrella of “healthy,” in my opinion.
But pregnancy cravings hit hard, and that bread came in visions. So I had to find a solution.
Looking in my freezer, I had almond flour and flax seed meal. I also had a spare banana, half a cup of homemade applesauce to use up, and plenty of eggs.
I began to plan and pour and mix, and the happy result was this delicious recipe.
My second-oldest child immediately gobbled up two muffins fresh from the oven, while his one-year-old sister ate a muffin-and-a-half within ten minutes. And there was zero guilt in my mama heart because I knew that the ingredients were all wholesome and nutritious–foods I’d want my children to eat for their health.
Sugar-Free Chocolate Brownie Muffins
How do you sweeten chocolate muffins without using white sugar or brown sugar? There are so many natural sweetener options!
Here are a few natural sweeteners used in this recipe:
- Applesauce
- Ripe banana
- Maple syrup (honey would also be an acceptable substitute, though maple syrup has a slightly lower glycemic index)
Gluten-Free Chocolate Muffins with Almond Flour
The almond flour used in this recipe not only increases the nutritional value of these muffins, but it also makes them gluten-free and higher in protein and healthy fats.
Tools You Need to Bake Healthy High-Protein Chocolate Brownie Muffins
- A 12-cup muffin pan (our favorite is the Trudeau structure silicone muffin pan, which makes removing the baked muffins a breeze)
- A mixing bowl
- A spatula
- Measuring cups
- Measuring spoons

Ingredients for High-Protein Chocolate Brownie Muffins
- 1 egg
- 1/2 cup organic peanut butter
- 3/4 cup unsweetened applesauce
- 1 mashed ripe banana (about 1/2 cup)
- 1/4 cup coconut oil (in liquid state)
- 1/2 cup unsweetened plain Greek yogurt
- 1/2 cup organic maple syrup
- 1 Tbsp. pure vanilla extract
- 4 Tbsp. cocoa powder (dark chocolate, 100% cacao)
- 1 cup almond flour
- 2 Tbsp. organic flaxseed meal
- 1/4 tsp. sea salt
- 1/2 tsp. baking powder
- 1/4 tsp. baking soda
- 3 Tbsp. protein powder
- 1/2 cup chopped walnuts
- 1/2 cup chopped dark chocolate or dark chocolate chips
How to Make Healthy High-Protein Brownie Muffins
- Preheat oven to 350F.
- In a medium-sized mixing bowl, mix together all wet ingredients (egg, peanut butter, applesauce, banana, coconut oil, Greek yogurt, maple syrup, and vanilla extract) until no lumps remain and all ingredients are well-incorporated.
- In a separate bowl, mix together the cocoa powder, almond flour, flaxseed meal, sea salt, baking powder, baking soda, and protein powder.
- Add the dry ingredients to the wet ingredients. Add the chopped walnuts and dark chocolate. Mix until fully incorporated and no lumps or dry spots remain.
- Using a measuring cup, scoop the muffin batter into a silicone muffin pan.
- Bake at 350F for 15-18 minutes. The top of the muffin will not be firm to touch; because this muffin is ultra-moist, it should leave residue on your finger when touched.
- Let cool before removing from the pan. (These muffins are extremely moist and trying to remove them from the pan when they are too hot will result in broken or squished muffins.)
How to Store These Healthy Chocolate Muffins
Store in an airtight container in the refrigerator for up to 5 days. (Storing at room temperature will result in faster deterioration, because these muffins are very moist.)
Recipe Card

Healthy Chocolate Brownie Muffins (Almond Flour, High Protein)
Oh, goodness! These Healthy Chocolate Brownie Muffins (Almond Flour, High Protein) are so fudgy that they are basically brownies without any refined sugar. Only healthy ingredients, lots of protein, and natural sweeteners.
Ingredients
- 1 egg
- 1/2 cup organic peanut butter
- 3/4 cup unsweetened applesauce
- 1 mashed ripe banana (about 1/2 cup)
- 1/4 cup coconut oil (in liquid state)
- 1/2 cup unsweetened Greek yogurt
- 1/2 cup organic maple syrup
- 1 Tbsp. pure vanilla extract
- 4 Tbsp. cocoa powder (dark chocolate, 100% cacao)
- 1 cup almond flour
- 2 Tbsp. organic flaxseed meal
- 1/4 tsp. sea salt
- 1/2 tsp. baking powder
- 1/4 tsp. baking soda
- 3 Tbsp. protein powder
- 1/2 cup chopped walnuts
- 1/2 cup chopped dark chocolate or dark chocolate chips
Instructions
- Preheat oven to 350F.
- In a medium-sized mixing bowl, mix together all wet ingredients (egg, peanut butter, applesauce, banana, coconut oil, Greek yogurt, maple syrup, and vanilla extract) until no lumps remain and all ingredients are well-incorporated.
- In a separate bowl, mix together the cocoa powder, almond flour, flaxseed meal, sea salt, baking powder, baking soda, and protein powder.
- Add the dry ingredients to the wet ingredients. Add the chopped walnuts and dark chocolate. Mix until fully incorporated and no lumps or dry spots remain.
- Using a measuring cup, scoop the muffin batter into a silicone muffin pan.
- Bake at 350F for 15-18 minutes. The top of the muffin will not be firm to touch; because this muffin is ultra-moist, it should leave residue on your finger when touched.
- Let cool before removing from the pan. (These muffins are extremely moist and trying to remove them from the pan when they are too hot will result in broken or squished muffins.)
- Store in an airtight container in the refrigerator for up to 5 days. (Storing at room temperature will result in faster deterioration, because these muffins are very moist.)
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