If you are torn on what flavor muffins to make, why not try these delicious gluten free chocolate pumpkin muffins? These chocolate pumpkin marble muffins are the best of both worlds because the chocolate and pumpkin flavors are swirled together!

A gluten free pumpkin chocolate swirl muffin on a plate.

My kids laughed when I came up with this new muffin recipe. I think it is because they never saw a swirl or marbled cake growing up. They have been gluten free so long. They had never tried anything like this before.

If you are new to gluten free baking, I highly encourage you to try swirling different muffin or cake flavors together. This recipe was inspired by my famous gluten free chocolate cake and homemade gluten free pumpkin bread recipes. I toned down the sugar a bit to keep these more muffin-like.

If you keep the full sugar, you can make it into a gluten free chocolate pumpkin swirl cake.

I actually impressed with this recipe. I would definitely make this again. I’m still learning to cook gluten free recipes here.”

paige, blog comment
A chocolate pumpkin muffin cut in half on a plate.

Allergen Information:

This homemade pumpkin chocolate muffin recipe is gluten-free, nut-free, oat-free, and soy-free. These muffins can be made dairy-free with dairy-free yogurt and butter.

Check out all of my delicious gluten free pumpkin recipes on the blog.

Photos of the pumpkin chocolate muffins ingredients.

Ingredient Notes:

For the full list of ingredients and amounts, please go to the recipe card below.

  • Gluten-free flour blend: I tested this recipe using Bob’s Red Mill 1 to 1 Gluten-Free Flour Blend and King Arthur’s Measure for Measure Gluten-Free Blend. That doesn’t mean others will not work; I just have not tested other flours, and I can not guarantee the recipe will work if you use other mixes.
  • Xanthan gum – If your gluten free flour blend doesn’t contain xanthan gum or guar gum, please add one teaspoon.
  • Baking Powder – I recommend using aluminum-free.
  • Pumpkin Puree – Be sure to use canned pumpkin and NOT pumpkin pie filling
  • Cocoa powder – Most brands are gluten free but always read the labels. I like Ghirardelli, Anthony’s Cocoa, and Hershey’s brands. Note Rodelle is no longer gluten free, as it has the potential to be made on shared equipment.
  • Eggs – Size large.
  • Yogurt – Use unflavored plain yogurt. You can also use dairy-free yogurt.
  • Non-dairy or regular milk is fine to use.
  • Butter or Oil – I use a combination in this recipe, but you can use one or the other. If you use butter, use unsalted.

I have tons of easy gluten free fall recipes for you to try this fall or any time!

Step-By-Step Photos and Directions:

Steps 1 and 2 photos to make these muffins.

Step 1: Add the dry ingredients to a large mixing bowl and whisk to blend them. Add the wet ingredients in a separate smaller bowl and whisk them together.

Mix the wet and dry ingredients together, being careful NOT to overmix the batter. This will make your muffins light and fluffy!

👀 Sandi Says: I do NOT recommend using a standing mixer. It will overmix your batter, and you will not get fluffy muffins.

Step 2: Repeat with the pumpkin ingredients. Again, be careful not to overmix your batter.

Photos of steps 3 and 4 making muffins.

📢 Sandi says: Every gluten-free flour blend has a different starch-to-grain ratio. The brand of gluten-free flour you use will affect the moisture of the batter. If your cake batter is too runny, add more flour, and if it is too thick, add more liquids.
Read Why Gluten-Free Flour Blends Vary to learn more about this.

Step 3: Place parchment paper muffin liners in each section of a muffin pan and fill half with the pumpkin batter and half with the chocolate batter.

Step 4: Use a knife to swirl the two batters together gently.

Step 5: Bake the muffins at 350º F for 20-25 minutes. Remove and place the muffins on a cooling rack.

To test for doneness, insert a toothpick into the center of a muffin. If the toothpick comes out clean, it is done baking. The muffins need to be baked longer if you see batter or crumbs.

Step 6: Remove the muffins carefully to a wire cooling rack. Enjoy when they cool off.

The top view of the pumpkin chocolate swirl muffins.

I have tons of delicious gluten free muffins recipes on the blog as well. They are perfect for breakfast time or as a healthy snack!!

Try these flavor variations!

  • Make a pumpkin spice icing by mixing 1/2 cup powdered sugar with 1/2 teaspoon pumpkin pie spice and 2 TBSP of water. Mix well and drizzle.
  • Add chocolate chips to the chocolate and pumpkin halves.
  • You can add pecans or walnuts.
Drizzling pumpkin spice icing over the muffin.

You may also love these Gluten Free Pumpkin Cream Cheese Muffins.

Frequently Asked Questions:

How do you get a dome top on muffins?

If you want your muffins to have a domed top, bake at 425º ° F for the first 5 minutes, then reduce the temperature to 350º F.

Do you have to swirl the two flavors together?

Nope. You can make these as separate muffin flavors or more block-style, like the photo of the muffin cut in half.

Is canned pumpkin the same as pumpkin puree?

Canned pumpkin is pretty much the same as pumpkin puree. Pumpkins are roasted and then pureed to have a fine texture.

What makes a muffin light and fluffy?

The biggest secret to light and fluffy muffins is to not overmix your batter. I never use a standing mixer to make muffins; it makes them dense.

How do you prevent sticky or gummy muffins?

Add a little dry, uncooked rice to the bottom of each muffin tin. Add the muffin paper on top of it. The rice will absorb the extra moisture, helping to prevent your muffins from being gummy or sticky.

How long will these muffins keep fresh?

These muffins will keep fresh for up to 4 days in an airtight container or up to 4 months in the freezer.

More Gluten Free Fall Recipes:

Love This Recipe?

If you made and enjoyed this recipe, I would be incredibly grateful if you could leave a comment below. Please include which flour blend you used. This will help others know this recipe is delicious. Thank you!

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 4 votes
gluten free allergy icon
nut free allergen icon
soy free allergy icon
vegetarian icon
Prep Time 20 minutes
Cook Time 20 minutes
Total Time 40 minutes
Course Gluten Free Breakfast Recipes, 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 aluminum-free
  • ½ teaspoon baking soda
  • dash of salt
  • ½ teaspoon pumpkin spice
  • 1 teaspoon ground cinnamon
  • cup brown sugar
  • 1 large egg
  • ½ cup pumpkin puree
  • ¼ cup full fat yogurt
  • ¼ cup light oil
  • ¼ cup non-dairy or regular milk

Chocolate Muffin Batter:

  • 1 teaspoon pure vanilla extract
  • cup cane sugar
  • cup cocoa powder
  • cup gluten free flour blend
  • 1 teaspoon baking powder aluminum-free
  • dash salt
  • 1 large egg
  • ¼ cup unsalted 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 1/4 cup of powdered sugar, 1/2 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 airtight container, or up to 4 months in the freezer.


Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, you may need to adjust your moisture levels in your baked goods.


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
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Nutrition Disclaimer

Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.

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Recipe Rating


  1. 5 stars
    I actually impressed with this recipe. I would definitely make this again. I’m still learning to cook gluten free recipes here. I would love to see you to adjust some stuff like muffins where pumpkin side are so soft texture and choc side is cake like and I would love to know how to make choc side more softer if you know the tips. It would be great to include the tips on this website. I also made pumpkin cookies of yours. Omg! Delicious! You have made me stay motivated and learn how to love the kitchen more. 💜💜💜

    1. I am so glad you loved the recipe! I suspect the chocolate side is a little more dense because of the melted chocolate. You could add 1 teaspoon additional aluminum-free baking powder so it fluffs more. (It must be aluminum-free to avoid an aftertaste.) Also be sure you are not overmixing the batter.