Incredible Gluten Free Chocolate Pumpkin Swirl Muffins

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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 pumpkin chocolate swirl muffin on a plate.

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Ingredient Notes:
Step By Step Recipe Directions:
Variations:
Tips and Recipe FAQ:
More Gluten Free Fall Recipes:
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Fearless Dining
💬 Comments

My kids sort of 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 too!

You will love the flavors of these muffins. They are easy to freeze, so you always have a grab-and-go breakfast!

A chocolate pumpkin muffin cut in half on a plate.

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

Top Pick

King Arthur, Measure for Measure Flour 3 lbs

This is one of my favorite gluten-free flour blends for cookies, cakes, pie crust, biscuits, and muffins! (Do not use this flour blend for yeast recipes.)

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Ingredient Notes:

Photos of the pumpkin chocolate muffins ingredients.

Gluuten 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 Recipe 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!

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

Step 2: Do the same with the pumpkin ingredients. Again be super careful not to overmix your batter.

Step 3: Put muffin liners into each muffin section and fill each 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.

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!!

Variations:

Make a pumpkin spice icing by mixing ½ cup powdered sugar with ½ teaspoon pumpkin pie spice and 2 tablespoon 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.

Tips and Recipe FAQ:

TIP: Use parchment paper muffin liners so your muffins don't stick to the paper!

How do you get a dome top on muffins?

If you want your muffins to have a domed style 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 make them 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 the muffins turn out 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 air-tight container or up to 4 months in the freezer.