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+ servings
a pumpkin chocolate swirl muffin on a plate

Gluten Free Chocolate Pumpkin Muffins

Sandi Gaertner
A moist delicious gluten free chocolate and pumpkin muffins recipe. If you haven't had a swirled muffins, it is the best of two different muffins recipes swirled into one!
5 from 3 votes
Prep Time 20 mins
Cook Time 20 mins
Total Time 40 mins
Course Gluten Free Muffins Recipes
Cuisine American
Servings 12 muffins
Calories 254 kcal


Pumpkin Muffin Batter:

  • 1 cup gluten free flour blend * see note
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • dash of salt
  • ½ teaspoon pumpkin spice
  • 1 teaspoon ground cinnamon
  • cup brown sugar
  • 1 egg
  • ½ cup pumpkin puree
  • ¼ cup full fat yogurt
  • ¼ cup light oil
  • ¼ cup almond milk

Chocolate Muffin Batter:

  • 1 teaspoon pure vanilla extract
  • cup sugar
  • cup cocoa powder
  • cup gluten free flour blend
  • 1 teaspoon baking powder
  • dash salt
  • 1 egg
  • ¼ cup butter melted
  • ¼ cup full-fat yogurt
  • ¼ cup non-dairy or regular milk


  • Preheat the oven to 350º F.

Pumpkin Muffin Batter:

  • Add the pumpkin muffins dry ingredients to a bowl and whisk to blend.
  • In a second bowl, add the pumpkin wet ingredients and mix well.
  • Pour the wet ingredients over the dry ingredients and mix. (*See note)

Chocolate Muffins

  • Add your dry chocolate muffins ingredients to a bowl and whisk to blend.
  • In a second bowl, add the wet ingredients and mix.
  • Pour the wet ingredients into the dry ingredients and mix. (*See note)
  • Add muffin papers to a muffin tin and add some chocolate muffin batter.
  • Add some pumpkin batter next to the chocolate batter.
  • Repeat so all of the muffin papers are full.
  • Take a knife and insert it into the batter and swirl gently to slighly swirl the batters together.
  • Optional: Sprinkle chocolate chips over the top and sightly press them into the batter.
  • Bake the muffins for 20-22 minutes. Remove the muffins and test with a toothpick for doneness. (*See note)
  • Remove from the oven and cool on a baking rack.


  1. I have tested this recipe with King Arthur Measure for Measure GF and Bob's Red Mill 1 to 1 GF blend. That doesn't mean others will not work, I just have not tested other flours.
  2. If your gluten free flour blend doesn’t contain Xanthan Gum or Guar Gum, please add 1 teaspoon.
  3. To keep these muffins light and fluffy, mix your wet and dry ingredients until it is just barely mixed. Over-mixing can make your muffins a lot denser.
  4. To test to see if your muffins are baked, insert a toothpick into the middle of a muffin. If the toothpick comes out clean, your muffins are done baking. If you see batter or crumbs on the toothpick, it needs to bake a little longer.
  5. Optional: Top with pumpkin spice icing by combining ¼ cup of powdered sugar, ½ teaspoon of pumpkin pie spice, and 1-2 teaspoons of milk (or non-dairy milk). Whisk to blend.
  6. These muffins will keep up to 3 days in an air-tight container, or up to 4 months in the freezer.


Serving: 12muffinsCalories: 254kcalCarbohydrates: 40gProtein: 4gFat: 11gSaturated Fat: 4gPolyunsaturated Fat: 1gMonounsaturated Fat: 5gTrans Fat: 1gCholesterol: 39mgSodium: 114mgPotassium: 207mgFiber: 4gSugar: 25gVitamin A: 1757IUVitamin C: 1mgCalcium: 91mgIron: 2mg
Keyword chocolate pumpkin muffins, gluten free marble muffins
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