Vegan Chocolate Pumpkin Swirl Muffins

Do I really need to even talk about these muffins?

No? Okay…

A closeup shot of a batch of vegan squash puree and chocolate swirl muffins.

No, wait. I need to. I can’t not talk about them. I mean, come on. Pumpkin! Chocolate! IN A SWIRL?!

I can’t believe it’s fall already. When did that happen?? I think that since I’m not in school anymore and I don’t have any kids in school (or any kids at all, nope, thanks) I sometimes lose track of where the year goes.

Side view of a stack of vegan chocolate muffins made with squash puree for fall.

I mean, when you’re in school, all of the holidays are just that much more important because you get VACATION! Thanksgiving break! Winter break!

But, now that I’m all grown up, all that excitement has pretty much waned. I’m not a big holiday person, mostly because they seem to pop up on me, like oh, hey! Wait – Thanksgiving is tomorrow?!

Yeah. It’s pretty awkward sometimes.

Especially when we’re in the thick of fall and I’ve barely cracked the lid on my pumpkin spice or have yet to make any pumpkin recipes so far this year. And Halloween is just around the corner.

Top-down view of the flour, squash puree, and other ingredients necessary to make pumpkin muffins.

But wait. I am here for redemption! Because this recipe totally makes up for my lack of pumpkin recipes thus far. This if for two reasons:

1. It’s got chocolate in it. Chocolate+pumpkin=❤.


Could these be any prettier?

Top-down view of a can of pumpkin puree with a semi-shallow depth of field.

This recipe is just a teeny tiny bit annoying because you have to mix things together and then split them up into separate bowls. If you use a kitchen scale, your life will be way easier – just weigh the ingredients as you put them in the bowl, then take out half. If you don’t use a scale, just eyeball it.

The chocolate mixture has a bit of extra sugar because the cocoa needs it. I tried making these without the extra sugar, and was not a huge fan. But extra sugar = extra ❤.

Also, the chocolate chips are necessary, and delicious.

Top-down view of a single chocolate pumpkin swirl muffin on a white porcelain plate.

If you’re short on time and patience, you can totally make these without swirling them. But if you want to impress all of your fall-pumpkin-loving friends, make the swirl.

This giant recipe makes 18 muffins. Eighteen! That means you can make them, sequester 6 of them for yourself, go hide in a closet and eat them all at once (guilty), and STILL impress your Halloween-obsessed PSL-fan friends with a “full” batch of vegan chocolate pumpkin swirl muffins.

Top-down view of a dozen chocolate and squash puree swirl muffins on a black platter sitting on a cream and white tablecloth.

Wait, I totally just sneaked that in there. Did I mention these are vegan? Win.

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Vegan Chocolate Pumpkin Swirl Muffins

  • Author: Raquel Smith
  • Total Time: 45 minutes
  • Yield: 18 muffins 1x


Nothing says fall like pumpkin baked goods. Add some chocolate to the equation and you’ve got yourself something special. These vegan-friendly chocolate pumpkin swirl muffins will knock your socks off, and are suitable for herbivores and carnivores alike.


  • 2 cups all-purpose flour
  • 1 cup whole wheat flour
  • 2 tsp cinnamon
  • 1/2 tsp nutmeg
  • 1/4 tsp ground cloves
  • 3/4 tsp salt
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 cup + 2 Tbsp cocoa powder
  • 3/4 cup + 1/3 cup vegan granulated sugar, divided
  • 2 Tbsp ground flax seed
  • 6 Tbsp water
  • 1/3 cup canola oil
  • 1 1/2 cups almond milk
  • 15 oz pumpkin puree (1 can)
  • 2/3 cup chocolate chips, divided


  1. Preheat oven to 350°F and grease a muffin tin. Combine the flax seed and water in a small bowl to make a flax egg, and set aside.
  2. Combine all the flours, spices, salt, baking powder, and baking soda in a medium-sized bowl. Remove half, using a scale if you have one, and place in another medium bowl.
  3. To just one of the bowls, add the cocoa powder and sift to remove all clumps. Add 1/3 cup sugar only to the bowl with the cocoa powder and stir to combine. Add 1/3 cup chocolate chips to each bowl and stir to combine.
  4. In a large bowl, combine the remaining 3/4 cup sugar, flax egg, canola oil, almond milk, and pumpkin puree. If you have a kitchen scale, weigh all these ingredients together as you put them in the bowl – this will make dividing it easier. Whisk well.
  5. Measure a little more than half of the pumpkin mixture into the bowl with the cocoa mixture and stir together. Add the remaining pumpkin mixture to the remaining dry ingredients in the other bowl, and stir just until no lumps remain.
  6. Spoon about 1 tablespoon of the chocolate mixture into each cup of a muffin tin. Add an equal amount of the non-chocolate mixture, then use a toothpick to swirl together. Add another bit of chocolate, then a spoonful of pumpkin, and swirl again. Repeat if necessary, until the cups are about 2/3 full.
  7. Bake for 22-24 minutes, until a toothpick inserted in the center comes out clean. Remove from the muffin tin onto a cooling rack and let cool.


Out of oil? No problem – try these creative substitutions.

  • Prep Time: 20 mins
  • Cook Time: 25 mins
  • Category: Muffins
  • Method: Baking
  • Cuisine: Breakfast

Keywords: Pumpkin, Chocolate, Halloween, Fall, Autumn, baked goods

Are you more of a nut person when it comes to your baked goods? Save this recipe for later, and make our pumpkin nut muffins instead!

Clearly, someone has a muffin fetish! Be sure to check out all of our favorite vegan muffin recipes including:

And if you loved this one, give it a rating in the comments below!

Photos by Raquel Smith, © Ask the Experts, LLC. ALL RIGHTS RESERVED. See our TOS for more details. Originally published on October 26, 2015. Last updated: October 6, 2021 at 11:23 am.

Nutritional information derived from a database of known generic and branded foods and ingredients and was not compiled by a registered dietitian or submitted for lab testing. It should be viewed as an approximation.

About Raquel Smith

Raquel is a whole foods enthusiast, an avid mountain biker, and a dog lover. She works by day at Food Blogger Pro and formerly maintained her food blog "My California Roots" (now merged into Foodal).

12 thoughts on “Vegan Chocolate Pumpkin Swirl Muffins”

  1. Yum! I just saw these on FoodGawker. I love pumpkin + chocolate. It’s such an unusual combination, but it works. Pinned to make ASAP!

    • Thanks so much, Lucy! I’ve always loved chocolate chips in pumpkin muffins, so I decided to go all-in with the chocolate. I hope you enjoy them!

  2. Raquel these look so amazing! My two favorite flavors all in one, so happy. Your photos are so gorgeous, keep it going girl!

    • Hi Maria! You could certainly try, though since I haven’t made it that way I can’t guarantee it would turn out. I would guess you’d need to add some extra liquid, maybe 1/4-1/2 cup to get it to turn out right. If you try it be sure to let me know!

  3. Made these today and they are both gorgeous and delicious! The extra time and effort required for the aesthetics is so worth it!


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