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chocolate pumpkin muffin with marbled look

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.

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
Servings 12 muffins
Calories 198 kcal
Author Monique Volz of AmbitiousKitchen.com


  • 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, allspice 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 Facts
Healthy Marbled Chocolate Pumpkin Muffins
Amount Per Serving (1 muffin)
Calories 198 Calories from Fat 83
% Daily Value*
Fat 9.2g14%
Saturated Fat 6.5g41%
Carbohydrates 29.1g10%
Fiber 4.3g18%
Sugar 14.2g16%
Protein 3.2g6%
* Percent Daily Values are based on a 2000 calorie diet.