Healthy Marbled Chocolate Pumpkin Muffins

Incredibly fluffy marbled chocolate pumpkin muffins swirled with pumpkin spice batter and double chocolate batter. These muffins are made with wholesome ingredients and make the perfect snack or healthier treat.

Prep Time
15 mins
Cook Time
20 mins
Total Time
35 mins

photo of a healthy marbled chocolate pumpkin muffin with text underneath

Welcome to the annual #AKPumpkinWeek where we celebrate all things pumpkin related and do a fun giveaway to kick off the season. I’m super excited to bring you these chocolate pumpkin muffins because quite frankly… THEY MIGHT JUST BE THE BEST MUFFINS I’VE EVER MADE.

All caps necessary indeed.

healthy marbled pumpkin muffins in a muffin tin

They’re moist, full of both chocolate and pumpkin flavor and taste more like a fluffy cupcake than a muffin. I would like to live in these little swirls. YASSS.

If you’re ready to cozy into fall weather, bake your heart out and fill your home with the best smelling spices around, then get ready for a week full of delicious nourishing recipe. This year, we’re doing both sweet and savory, which means you’ll have something to make for breakfast, lunch, dinner and dessert. So let’s do this thang.

chocolate muffin batter and pumpkin muffin batter in two separate bowls to make chocolate pumpkin muffins

These marbled chocolate pumpkin muffins start by making one batter, then you’ll divide it evenly into two bowls and add a little cocoa powder to one of the batters.

Once you’ve done that you can alternate adding the batter to muffin liners.

swirling batter for chocolate pumpkin muffins in a muffin tin

Then you’ll use a knife and swirl the batter just a few times. Don’t over do it or your batter will look all mixed together. We want to keep them pretty.

Before baking, don’t forget to top them with a few million dollar chocolate chips if you know what’s good.

chocolate pumpkin muffins in a muffin tin

Bake them up. They’ll be glorious, I promise.


chocolate pumpkin muffins on a grey board

I MEAN JUST LOOK AT THESE. How could you not want to bake them?

They’re beautiful, satisfying and even freezer friendly.

chocolate pumpkin muffin with a bite taken out

See how to make the chocolate pumpkin muffins:

More pumpkin recipes you’ll love:

Pumpkin Chocolate Chip Muffins

Healthy Pumpkin Pancakes

Slow Cooker Black Bean Pumpkin Turkey Chili

Pumpkin Paleo Brownies

Paleo Pumpkin Pie Bars

Healthy Marbled Chocolate Pumpkin Muffins

5 from 11 votes
chocolate pumpkin muffins on a grey board
Course Breakfast, Dairy Free, Muffin, Snack
Keyword chocolate pumpkin muffins
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Serves 12
Incredible marbled chocolate pumpkin muffins swirled with pumpkin spice and rich chocolate. These muffins are made with wholesome ingredients and make the perfect snack or healthy treat.


  • 1 cup pumpkin puree
  • 1/2 cup pure maple syrup
  • 2 large eggs, at room temperature
  • 1/4 cup unsweetened almond milk (or milk of choice)
  • 1 teaspoon vanilla extract
  • 1 1/2 cups whole wheat pastry flour
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1/2 teaspoon nutmeg
  • 1/2 teaspoon ground ginger
  • 1/4 teaspoon allspice
  • 1/2 teaspoon salt
  • 1/4 cup coconut oil, melted and cooled (or sub melted butter)
  • 1/4 cup unsweetened cocoa powder
  • 1/2 cup chocolate chips, divided


  1. Preheat oven to 350 degrees F. Line a 12 cup muffin tin with liners and spray the inside of the liners with nonstick cooking spray.
  2. In a large bowl, mix together pumpkin, maple syrup, eggs, almond milk and vanilla extract.
  3. In a separate large bowl, whisk together the dry ingredients: whole wheat pastry flour, baking soda, cinnamon, nutmeg, ginger, cloves and salt. 
  4. Add dry ingredients to wet ingredients and mix until just combined. Next, stir in melted coconut oil.
  5. Divide batter in half; adding half of the batter to a seperate medium bowl. Stir in cocoa powder and ¼ cup chocolate chips into one of the batters, mixing until just combined.
  6. First spoon a less less than 1 tablespoon of the pumpkin batter into each muffin liner and then spoon 1 tablespoon chocolate batter on top. Repeat until all of your muffin batter is gone. 
  7. Swirl the batters together with a knife, just about 3-4 times. Don’t go crazy or the batter won’t look nice and swirled. 
  8. Gently shake your muffin pan back and forth just a few times to even out the batter. Top batter with remaining chocolate chips.
  9. Bake for 20-25 minutes until a tester comes out clean. Mine were perfect at 22 minutes. Cool in pan for 10 minutes, then transfer to a wire rack to finish cooling.

Recipe Notes

To make the muffins gluten free: I recommend using Bob's Red Mill 1:1 gluten free flour. You can also substitute chickpea flour, but you may need to add a splash or two more milk to the batter.

To make muffins vegan: Use two flax eggs instead of regular eggs (2 tablespoons flaxseed meal + 6 tablespoons water). Please also be sure to use vegan chocolate chips (Enjoy Life is a great brand).

Feel free to make this recipe into bread! Just layer the batter in a greased 8x4 inch loaf pan. Bake for 45-55 minutes or until tester comes out clean or with just a few crumbs attached.

Servings: 12 muffins
Serving size: 1 muffin
Calories: 198kcal
Fat: 9.2g
Saturated fat: 6.5g
Carbohydrates: 29.1g
Fiber: 4.3g
Sugar: 14.2g
Protein: 3.2g


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