These Chocolate Peanut Butter Muffins are the perfect balance of indulgent flavor and wholesome ingredients. With whole-grain flour, applesauce instead of oil, and a mix of chocolate and peanut butter chips, they’re moist, fluffy, and just sweet enough for breakfast or a snack.
Why You’ll Love This Recipe
- Better-for-you ingredients: Uses whole wheat pastry flour and no added oil.
- Rich flavor: Combines chocolate and peanut butter in every bite.
- Kid- and family-friendly: A satisfying treat that still feels nourishing.
- Freezer-friendly: Great to make ahead and freeze for easy mornings.
Ingredients
Dry Ingredients:
- ¾ cup whole wheat pastry flour (or 1-to-1 gluten-free all-purpose flour)
- ⅓ cup + 1 tbsp unsweetened cocoa powder
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ¼ teaspoon fine sea salt
Wet Ingredients:
- ¾ cup applesauce (or well-mashed banana)
- ¼ cup pure maple syrup
- ¼ cup granulated sugar (cane, coconut, date, etc.)
- ½ cup creamy all-natural peanut butter
- 1 large egg
- ½ teaspoon vanilla extract
- ½ cup unsweetened non-dairy milk (Fit Mitten Kitchen uses cashew)
- ⅔ cup dark chocolate chips (or mix in peanut butter chips too)
Directions
- Preheat & prep
Preheat your oven to 375°F (190°C). Grease a 12-cup muffin tin or line it with paper liners. - Mix dry ingredients
In a medium bowl, whisk together the whole wheat pastry flour, cocoa powder, baking soda, baking powder, and salt until fully combined. - Whisk wet ingredients
In a large bowl, whisk applesauce, maple syrup, and granulated sugar until smooth. Add the peanut butter and whisk again until it’s well blended. Then whisk in the egg and vanilla extract until the mixture is smooth and consistent. - Combine wet + dry
Add the dry ingredients into the wet mixture gently using a spatula. Stir just a few times to start combining. Then, pour in the non-dairy milk and fold gently again—avoid overmixing to keep muffins light. - Add chips
Fold in the dark chocolate chips (and peanut butter chips, if using) by hand until they are evenly distributed in the batter. - Portion batter
Use a scoop (or large spoon) to divide the batter evenly into the prepared muffin tin. Fill each cup about 2/3 full so there’s room for rising. - Bake
Bake for 18–20 minutes, or until a toothpick inserted in the center of a muffin comes out clean (or with just a few moist crumbs). - Cool
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.
Pro Tips and Variations
- Don’t overmix the batter. Stir only until the flour disappears. Overmixing leads to dense, tough muffins.
- Use room-temperature ingredients. Peanut butter, egg, and milk mix more smoothly when not cold.
- Scoop evenly. For bakery-style results, use a medium cookie scoop to create uniform muffins that rise evenly.
- Check doneness early. Cocoa-based muffins can overbake quickly. Start checking at the 17-minute mark.
- Add extra chocolate on top. Drop a few extra chocolate chips over each muffin before baking for a bakery-style look.
Variations
- Banana Chocolate Muffins: Swap applesauce for mashed ripe banana for richer flavor.
- Peanut Butter Swirl: Warm 2 tbsp peanut butter and drizzle over the batter before baking; swirl with a toothpick.
- Double Chocolate: Add 2 tbsp extra cocoa powder and ¼ cup extra chocolate chips.
- Gluten-Free: Use 1:1 gluten-free flour (as noted in your ingredients).
- Mocha Muffins: Add 1 tsp instant espresso powder to the dry ingredients.
Serving Suggestions
- Enjoy warm with a cold glass of milk or your favorite non-dairy alternative.
- Add a spread of peanut butter on top for extra richness.
- Serve with fresh berries for a balanced breakfast.
- Pair with coffee for a perfect morning treat.
Storage & Reheating
- Room temperature: Store in an airtight container for up to 3 days.
- Refrigerator: Lasts up to 6 days when chilled.
- Freezer: Freeze individually wrapped muffins for up to 3 months.
Reheating
- Microwave: Warm for 10–15 seconds.
- Oven: Reheat at 300°F (150°C) for 5–7 minutes for a freshly baked texture.
Notes
- Batter will be thick—this is normal for cocoa + peanut butter mixtures.
- If using natural peanut butter, stir very well before measuring.
- Dark chocolate chips melt beautifully and give a richer flavor, but semisweet works too.
FAQs
Can I make these muffins without peanut butter?
Yes! Replace peanut butter with almond or cashew butter.
Can I make them egg-free?
Yes — use a flax egg (1 tbsp ground flax + 3 tbsp water). Allow to gel for 5 minutes.
Why did my muffins turn out dry?
They were likely overbaked or the flour was overmeasured. Spoon and level flour instead of scooping.
Can I use dairy milk?
Absolutely — any milk works.
Can I reduce the sugar?
You can reduce the granulated sugar by 2 tbsp without affecting texture.
Conclusion
Healthy Chocolate Peanut Butter Muffins are soft, moist, chocolatey, and packed with wholesome ingredients that you can feel great about. Whether you serve them for breakfast, snack time, or meal prep for the week, they’re always a hit. Freeze well, reheat beautifully, and make mornings easier and more delicious.


Healthy Chocolate Peanut Butter Muffins
- Total Time: 30 minutes (Prep + Bake)
- Yield: 12 muffins 1x
Description
Moist muffins made with whole-grain flour, applesauce, chocolate + peanut butter chips — healthier breakfast treat.
Ingredients
Dry Ingredients:
- ¾ cup whole wheat pastry flour (or 1-to-1 gluten-free all-purpose flour)
- ⅓ cup + 1 tbsp unsweetened cocoa powder
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ¼ teaspoon fine sea salt
Wet Ingredients:
- ¾ cup applesauce (or well-mashed banana)
- ¼ cup pure maple syrup
- ¼ cup granulated sugar (cane, coconut, date, etc.)
- ½ cup creamy all-natural peanut butter
- 1 large egg
- ½ teaspoon vanilla extract
- ½ cup unsweetened non-dairy milk (Fit Mitten Kitchen uses cashew)
- ⅔ cup dark chocolate chips (or mix in peanut butter chips too)
Instructions
Preheat & prep Preheat your oven to 375°F (190°C). Grease a 12-cup muffin tin or line it with paper liners.
Mix dry ingredients In a medium bowl, whisk together the whole wheat pastry flour, cocoa powder, baking soda, baking powder, and salt until fully combined.
Whisk wet ingredients In a large bowl, whisk applesauce, maple syrup, and granulated sugar until smooth. Add the peanut butter and whisk again until it’s well blended. Then whisk in the egg and vanilla extract until the mixture is smooth and consistent.
Combine wet + dry Add the dry ingredients into the wet mixture gently using a spatula. Stir just a few times to start combining. Then, pour in the non-dairy milk and fold gently again—avoid overmixing to keep muffins light.
Add chips Fold in the dark chocolate chips (and peanut butter chips, if using) by hand until they are evenly distributed in the batter.
Portion batter Use a scoop (or large spoon) to divide the batter evenly into the prepared muffin tin. Fill each cup about 2/3 full so there’s room for rising.
Bake Bake for 18–20 minutes, or until a toothpick inserted in the center of a muffin comes out clean (or with just a few moist crumbs).
Cool Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.
Notes
- Batter will be thick—this is normal for cocoa + peanut butter mixtures.
- If using natural peanut butter, stir very well before measuring.
- Dark chocolate chips melt beautifully and give a richer flavor, but semisweet works too.
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Category: Breakfast, Snacks
- Method: Baking
- Cuisine: American
Keywords: Chocolate Peanut Butter Muffins