Marbled Chocolate Pumpkin Muffins - Cooking Up Clean

Marbled Chocolate Pumpkin Muffins

marbled chocolate pumpkin muffins

I was never one to devour the bread basket at a restaurant as bread just isn’t really my thing.    Except for at breakfast. Then, gimme some bready, moist, warm, fresh from the oven muffins and I’m one happy girl!  It used to be a weekend tradition with my husband that we’d make a batch of muffins together every Saturday and savor each bite with our morning cup of joe.  This has continued throughout nearly ten years of marriage and our kiddos also love weekend muffins.  When I first started out on this clean eating adventure, I was a little disheartened to think that muffins were probably off the list for good.  Breakfast was (and still is) my most challenging meal of the day to keep clean.  Traditional breakfast items are usually full of sugar, wheat or dairy, all of which I’m trying to either avoid or minimize.  I’ve come up with a go-to muffin base that can be changed up depending on what the muffin flavor-of-the-day might be. 

marbled chocolate pumpkin muffins

Last fall, I hand-scratched this recipe on a random piece of printer paper as one of my first recipes ever created.  Marbled chocolate pumpkin muffins remind me of the holidays so this is a perfect time to share them with you.  Warm and moist right out of the oven, the chocolate marbling is still gooey like fresh melted chocolate.  Muffins make me happy, I hope they make you happy too 🙂

marbled chocolate pumpkin muffins

Marbled Chocolate Pumpkin Muffins
Prep time
Cook time
Total time
Recipe type: Breakfast
Cuisine: paleo, gluten-free, dairy-free
Serves: 12
  • 5 eggs, separated
  • ½ cup pumpkin puree
  • ¼ cup melted coconut oil
  • ½ cup maple syrup
  • 1 teaspoon vanilla
  • 2 tablespoons coconut milk (or almond milk)
  • ½ cup coconut flour
  • ¼ cup tapioca flour
  • 1 teaspoon baking soda
  • 2 teaspoons baking powder
  • ¼ teaspoon salt
  • 1 teaspoon cinnamon
  • ½ teaspoon nutmeg
  • ¼ teaspoon cloves
  • ¼ teaspoon ginger
  • ⅓ cup melted chocolate chips
  1. Preheat oven to 350 degrees.
  2. Lightly grease muffin pan with coconut oil.
  3. Separate the eggs and place egg whites aside in another bowl.
  4. In a medium bowl, combine egg yolks, pumpkin, oil, syrup, vanilla and coconut milk and whisk until smooth.
  5. In a separate bowl, combine all dry ingredients.
  6. Pour wet ingredients into dry and stir well.
  7. Beat egg whites until soft peaks form and stir into muffin batter.
  8. Scoop batter into muffin pan so each well is about ⅔ full.
  9. Melt chocolate chips and pour a small equal amount in the center of each muffin.
  10. With a butter knife, swirl the chocolate through the batter a few times and pull batter up from bottom to get marbling throughout.
  11. Bake for 35-40 minutes until golden.
Psst... this also makes up great as a breakfast bread in a loaf pan!


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