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Healthy Chocolate Peanut Butter Muffins

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4.80 from 5 votes
Taylor KiserBy Taylor Kiser
Taylor Kiser
Taylor Kiser Founder of Food Faith Fitness

Taylor Kiser is a Certified Personal Trainer and Nutrition Coach and a lover of health and fitness. A follower of Christ. Recipe developer. Photographer. Obsessed with cookie dough, pink & leop…

Expertise: Healthy Food View all posts →
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These Healthy Chocolate Peanut Butter Muffins are packed with peanut butter chips and made a little more wholesome with whole-wheat flour and Greek yogurt!

a hand holding healthy chocolate peanut butter muffins that are ripped in half

If there was ever a flavor combo destined to be together, sent from above, it’s chocolate and peanut butter. Mr. Harry Burnett Reese clearly knew this too when he created Reese’s Peanut Butter Cups back in 1928! No wonder these treats rank among the country’s top ten favorite candies. Chocolate and peanut butter are an iconic duo. The nutty, sweet-but-salty, sticky goodness of peanut butter paired with the rich, indulgent decadence of chocolate—it’s unbeatable!

So, can you blame me for coming up with this muffin recipe? And guess what? I made them just a little more wholesome than your average muffin. That way, you can have one for breakfast and no one will judge! And even if they do, who cares! These healthy chocolate-peanut butter muffins are such a delicious way to satisfy that craving for this classic combo every single time!

Are These Chocolate Peanut Butter Muffins Healthy?

Made with white whole-wheat flour, these muffins are a little more wholesome than those made with plain white flour. We don’t use any butter or oil here, just peanut butter and Greek yogurt to make them irresistibly moist. Though we use coconut sugar in this recipe, bear in mind that it doesn’t differ much from regular white sugar in terms of calories and how it affects blood sugar levels. Here, we use it mainly for taste. Coconut sugar adds notes of caramel to the muffins.

The recipe can easily be made vegan by using a plant-based yogurt and a flax “egg.” In a small bowl, mix one tablespoon of flax meal with three tablespoons of water. Leave this for ten minutes until it becomes gelatinous, and use instead of the egg. If needed, you can also use a 1:1 gluten-free flour instead of the white whole-wheat flour.

What Is White Whole-Wheat Flour?

Yes, I know it sounds like an oxymoron, but if you’re looking for a good way to boost the fiber of baked goods without having to use whole-wheat flour (which can make them stodgy and dense), white whole-wheat flour is the solution. Made from hard white wheat, rather than the hard red wheat of traditional whole-wheat flour, it has a milder flavor and lighter color. This makes it quite similar to all-purpose flour while retaining the nutritional benefits of whole grains. White whole-wheat flour is a superb choice for baking because it provides a more subtle flavor and lighter texture than regular whole-wheat flour.

12 peanut butter muffins on a cooling rack

How To Make Ahead and Store

Homemade muffins are best stored at room temperature, as they tend to dry out in the fridge. Once cooled, they can be stored in an airtight container for up to 4 days. Muffins can also be frozen in a Ziploc bag for up to 3 months.

healthy chocolate peanut butter muffins with a bite taken out of it

Serving Suggestions

Yes, I do eat these for breakfast, and when I do, I’ll pair them with an energizing Coffee Smoothie or an ice-cold Banana Smoothie.

If you’re like me and totally crazy about all things chocolate and peanut butter, why not try these healthy Peanut Butter Chocolate Chip Oatmeal Balls, or go for utter decadence with this Peanut Butter Chocolate Lava Cake Recipe?

Peanut butter chocolate chip muffins on a cooling rack

Recipe

Healthy Chocolate Peanut Butter Muffins

4.80 from 5 votes
Print Rate
Serves: 12
Prep: 10 minutes minutes
Cook: 20 minutes minutes
Chilling time: 30 minutes minutes
Total: 1 hour hour

Ingredients

  • 1 cup white whole-wheat flour
  • 1/4 cup unsweetened cocoa powder
  • 1 tablespoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 3/4 cup natural creamy peanut butter
  • 2/3 cup fat-free vanilla Greek yogurt
  • 3/4 cup coconut sugar
  • 10 tablespoons baking stevia
  • 1 egg
  • 2 teaspoons vanilla extract divided
  • 3/4 cup unsweetened vanilla almond milk
  • 1/2 cup peanut butter chips plus more for sprinkling

Instructions

  • Preheat oven to 400 degrees Fahrenheit and spray a muffin tin with cooking spray.
  • In a medium bowl, mix together the flour, cocoa powder, baking powder, baking soda, and salt. Set aside.
  • In a large, microwave-safe bowl, melt the peanut butter until smooth, about 1 minute. Whisk in the yogurt, stevia, coconut sugar, egg, vanilla extract, and milk until well combined.
  • Slowly fold the dry ingredients into the wet, followed by the peanut butter chips, stirring until just moistened. Cover and refrigerate 30 minutes.
  • Using an extra large cookie scoop (or just a spoon) divide the batter evenly across the greased muffin tin, filling each depression almost all the way to the top.
  • Sprinkle with extra peanut butter chips if desired and bake for 5 minutes. Then, reduce the oven temperature to 375 degrees Fahrenheit and bake another 14-16 minutes, or until a toothpick comes out clean.
  • Let the muffins cool in the pan for 5 minutes and then transfer to a cooling rack to finish cooling.
    Peanut butter chocolate chip muffins on a cooling rack
  • Devour!
    healthy chocolate peanut butter muffins with a bite taken out of it

Nutrition Info:

Calories: 198.8kcal (10%) Carbohydrates: 21.6g (7%) Protein: 7.5g (15%) Fat: 10.5g (16%) Saturated Fat: 2.3g (14%) Sodium: 128.5mg (6%) Fiber: 3g (13%) Sugar: 12.6g (14%)

Nutrition Disclaimer

Nutrition information are estimates only and may vary based on the specific brands, ingredients, and portion sizes you use. This data is provided for informational purposes only.

Author: Taylor Kiser
Course:Dessert, Snack
Cuisine:American
Share your creationsTag @foodfaithfit and hashtag it #foodfaithfitness so I can see what you made!
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About Taylor KiserHealthy Food

Taylor Kiser is a Certified Personal Trainer and Nutrition Coach and a lover of health and fitness. A follower of Christ. Recipe developer. Photographer. Obsessed with cookie dough, pink & leopard print.

Reader Interactions

Paola Westbeek

✓Reviewed by Paola WestbeekGastronomy & Fine Wines

Published: Oct 10, 2024 | Updated: Oct 17, 2025
4.80 from 5 votes (5 ratings without comment)

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