These Chocolate Peanut Butter Protein Muffins are made with Greek yogurt and swirled with peanut butter so each muffin contains over 5 grams of protein! While these are still a ‘dessert’ muffin, the added protein is a nice bonus!
Quick Tips
- Use a silicone muffin pan or cupcake liners to ensure that the muffins don’t stick to the pan
- I recommend using creamy peanut butter for the swirl, but regular or natural peanut butter will work!
- Top the muffins with a few extra chocolate chips before baking (if desired)

Equipment
- Hand or stand mixer
- Muffin pan
- Cupcake liners or non-stick spray (not needed if using a silicone muffin pan)
- Silicone spatula
- Measuring cups and spoons
- Cookie scoop (optional)
Ingredient Notes
- Plain Greek yogurt
- Vegetable or canola oil– olive oil would be an OK substitute for texture, but I have not tried it. It may negatively affect the taste
- Eggs
- Vanilla extract
- Brown sugar– light or dark brown sugar is OK
- All-purpose flour
- Cocoa powder
- Baking powder
- Baking soda
- Salt
- Chocolate chips
- Creamy peanut butter– regular or natural is OK
Love these Chocolate Peanut Butter Protein Muffins? Try these other muffin recipes!

How to make Chocolate Peanut Butter Protein Muffins
These chocolate peanut butter swirled muffins can be made using one bowl and just a handful of ingredients! Follow the steps below to make them.
- Make the chocolate muffin batter
- Add the peanut butter swirl and bake
How to make the chocolate muffin batter
Preheat the oven to 375 degrees. Use convection bake if you have it to help the muffins bake evenly!
Next, in a large mixing bowl, combine the brown sugar, oil and Greek yogurt. Use a hand or stand mixer to mix on low to medium speed until combined.
Add vanilla extract and eggs, then mix until combined.
Add salt, baking powder and baking soda. Mix until combined.
Add the cocoa powder and mix on low until combined (careful to mix slowly! cocoa powder can be messy).
Lastly, add the flour and mix until combined. Scrape down the bowl once complete.
Fold in ¾ cup of the chocolate chips and set the batter aside.
How to add the peanut butter swirl and bake
Prep the muffin tins by lining them with paper cupcake liners or spraying the pan with non-stick spray. If you are using a silicone muffin pan, you do not need to do this,
Use a small cookie scoop to measure out your batter – add one scoop to each muffin tin. Use a spoon to spread the batter throughout the bottom or tap it on the counter.
Spoon about a teaspoon of peanut butter over the batter. Do this for each muffin.
Use the small cookie scoop to add another full scoop into each tin, over the dollop of peanut butter.
Add another 1-2 teaspoons of peanut butter on top of each muffin, then use a toothpick or a butter knife to swirl the batter of each muffin.
Top each muffin with a few of the reserved chocolate chips and bake for 14-16 minutes or until a toothpick comes out clean.
Allow them to cool for 10-15 minutes before removing them from the pan, then enjoy!

If you loved these peanut butter muffins, try these other peanut butter-packed desserts!

Chocolate Peanut Butter Protein Muffins
Ingredients
Equipment
Method
- Preheat the oven to 375 degrees. Use convection bake if you have it.
- In a large mixing bowl, combine the brown sugar, oil and Greek yogurt. Use a hand or stand mixer to mix on low-medium speed until combined.
- Add vanilla extract and eggs. Mix until combined.
- Add salt, baking powder and baking soda. Mix until combined.
- Add the cocoa powder and mix on low until combined.
- Lastly, add the flour and mix until combined. Scrape down the bowl once complete.
- Fold in ¾ cup of the chocolate chips and set the batter aside.
- Prep the muffin tins by lining them with paper cupcake liners or spraying the pan with non-stick spray. If you are using a silicone muffin pan, you do not need to do this,
- Use a small cookie scoop to measure out your batter – add one scoop to each muffin tin. Use a spoon to spread the batter throughout the bottom or tap it on the counter.
- Spoon about a teaspoon of peanut butter over the batter. Do this for each muffin.
- Use the small cookie scoop to add another full scoop into each tin, over the dollop of peanut butter.
- Add another 1-2 teaspoons of peanut butter on top of each muffin, then use a toothpick or a butter knife to swirl the batter of each muffin.
- Top each muffin with a few of the reserved chocolate chips and bake for 14-16 minutes or until a toothpick comes out clean.
- Allow them to cool for 10-15 minutes before removing them from the pan, then enjoy!
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