Healthy Marbled Chocolate Pumpkin Muffins

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

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

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.

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.

healthy marbled pumpkin muffins in a muffin tin

Ingredients in healthy chocolate pumpkin muffins

These amazing, perfectly moist chocolate pumpkin muffins are made with wholesome ingredients you can feel good about. The pumpkin spice and dark chocolate combo is truly out of this world. Here’s what you’ll need:

  • Pumpkin puree: for that incredible pumpkin layer. Feel free to use canned pumpkin puree or make your own with this tutorial.
  • Maple syrup: we’re naturally sweetening these chocolate pumpkin muffins with a bit of pure maple syrup.
  • Eggs: you’ll need 2 eggs in this recipe. I have not tested these muffins with flax eggs but let me know if you do!
  • Almond milk: a bit of unsweetened almond milk adds the perfect amount of moisture. Feel free to use any milk you’d like.
  • Vanilla extract: always adding vanilla for delicious flavor.
  • Whole wheat pastry flour: I love baking with whole wheat pastry flour because it adds a boost of whole grains while keeping these muffins super fluffy. You can also use white whole wheat flour or a ratio of ¾ cup whole wheat flour + 1 cup all purpose flour.
  • Spices: the perfect mix of cozy fall spices comes from cinnamon, nutmeg, ground ginger & allspice.
  • Baking soda & salt: to help these muffins bake up properly.
  • Coconut oil: we’re using a little melted coconut oil for additional moisture. You can also use butter or vegan butter.
  • Unsweetened cocoa powder: be sure to use a high quality, unsweetened cocoa powder to get that amazing, rich chocolate flavor.
  • Chocolate chips: I love the bites of melted dark chocolate chips in these muffins. Feel free to use dairy free chocolate chips if you’d like.

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

How to “marble” double chocolate pumpkin muffins

  1. 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.
  2. Once you’ve done that you can alternate adding the batter to muffin liners.
  3. 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.
  4. Before baking, don’t forget to top them with a few million dollar chocolate chips if you know what’s good.

swirling batter for chocolate pumpkin muffins in a muffin tin

Tips for making chocolate pumpkin muffins

  • Follow the recipe. The best way to ensure the success of these easy, healthy chocolate pumpkin muffins is to follow the recipe and use the exact ingredients as written (unless I note specific substitutes).
  • Make sure your eggs are at room temperature. If your eggs are too cold you risk the coconut oil coagulating. To bring your eggs to room temp, simply place them in a bowl of warm water for 3-5 minutes before you use them. Also make sure your coconut oil has cooled after melting it.
  • Do not overmix the batter. If you overmix batter you’ll end up with muffins that are more dense and gummy instead of fluffy and soft. Plus, you want to be careful not to “over-swirl” the batters together.
  • Use fresh baking soda. If your baking soda is older than 3 months, I suggest grabbing a new one for best baking results.

double chocolate pumpkin muffins in a muffin tin

Customize your chocolate pumpkin muffins

  • 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).
  • Different mix-ins: feel free to add 1/2 chopped pecans or walnuts for a nutty version, or even unsweetened shredded coconut!

How to make marbled chocolate pumpkin bread

You can easily use this chocolate pumpkin muffins recipe for making a bread instead! Just layer the batter in a greased 8×4 inch loaf pan. Bake for 45-55 minutes or until tester comes out clean or with just a few crumbs attached.

healthy chocolate pumpkin muffins on a grey board

Freezer-friendly chocolate pumpkin muffins

These healthy marbled chocolate pumpkin muffins are freezer-friendly! Simply wrap muffins individually in freezer-safe bags or store them in a large freezer bag. When you’re ready to enjoy them, reheat for 30-45 seconds in the microwave or simply thaw them at room temperature.

chocolate pumpkin muffin with a bite taken out

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

SO DAMN GLORIOUS.

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

I hope you love these healthy marbled chocolate pumpkin muffins! If you make them be sure to leave a comment & a rating so I know how you liked them. Enjoy, xo!

Healthy Marbled Chocolate Pumpkin Muffins

4.94 from 15 votes
chocolate pumpkin muffins on a grey board
Course Breakfast, Dairy Free, Muffin, Snack
Cuisine American
Keyword chocolate pumpkin muffins, double chocolate pumpkin muffins, healthy chocolate pumpkin muffins, marbled chocolate pumpkin muffins
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Serves 12

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

Ingredients

  • 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

Instructions

  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.

To freeze: wrap muffins individually in freezer-safe bags or store them in a large freezer bag. When you’re ready to enjoy them, reheat for 30-45 seconds in the microwave or simply thaw them at room temperature.

Nutrition
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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