Tis the season to celebrate all things pumpkin related. Are you down?! Good. I’m super excited to bring you these chocolate pumpkin muffins because quite frankly…THEY MIGHT JUST BE THE BEST MUFFINS I’VE EVER MADE.
All caps necessary indeed.
They’re moist, full of both chocolate and pumpkin flavor and taste more like a fluffy cupcake than a muffin. I would like to live in these little swirls. YASSS.
If you’re ready to cozy into fall weather, bake your heart out and fill your home with the best-smelling spices around, then you’ve come to the right place for all of the delicious nourishing recipes.
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Ingredients in healthy chocolate pumpkin muffins
These amazing, perfectly moist chocolate pumpkin muffins are made with wholesome ingredients you can feel good about. The pumpkin spice and dark chocolate combo is truly out of this world. Here’s what you’ll need:
- Pumpkin puree: for that incredible pumpkin layer. Feel free to use canned pumpkin puree or make your own with this tutorial.
- Maple syrup: we’re naturally sweetening these chocolate pumpkin muffins with a bit of pure maple syrup.
- Eggs: you’ll need 2 eggs in this recipe. I have not tested these muffins with flax eggs but let me know if you do!
- Almond milk: a bit of unsweetened almond milk adds the perfect amount of moisture. Feel free to use any milk you’d like.
- Vanilla extract: always adding vanilla for delicious flavor. Learn how to make your own here!
- Whole wheat pastry flour: I love baking with whole wheat pastry flour because it adds a boost of whole grains while keeping these muffins super fluffy. You can also use white whole wheat flour or a ratio of ¾ cup whole wheat flour + 1 cup all purpose flour.
- Spices: the perfect mix of cozy fall spices comes from cinnamon, nutmeg, ground ginger & allspice.
- Baking soda & salt: to help these muffins bake up properly.
- Coconut oil: we’re using a little melted coconut oil for additional moisture. You can also use butter or vegan butter.
- Unsweetened cocoa powder: be sure to use a high quality, unsweetened cocoa powder to get that amazing, rich chocolate flavor.
- Chocolate chips: I love the bites of melted dark chocolate chips in these muffins. Feel free to use dairy free chocolate chips if you’d like.
Customize your chocolate pumpkin muffins
- To make the muffins gluten free: I recommend using Bob’s Red Mill 1:1 gluten free flour. You can also substitute chickpea flour, but you may need to add a splash or two more milk to the batter.
- To make muffins vegan: Use two flax eggs instead of regular eggs. Learn how to make flax eggs here! Please also be sure to use vegan chocolate chips (Enjoy Life is a great brand).
- Different mix-ins: feel free to add 1/2 chopped pecans or walnuts for a nutty version, or even unsweetened shredded coconut!
Tips for making chocolate pumpkin muffins
- Follow the recipe. The best way to ensure the success of these easy, healthy chocolate pumpkin muffins is to follow the recipe and use the exact ingredients as written (unless I note specific substitutes).
- Make sure your eggs are at room temperature. If your eggs are too cold you risk the coconut oil coagulating. To bring your eggs to room temp, simply place them in a bowl of warm water for 3-5 minutes before you use them. Also make sure your coconut oil has cooled after melting it.
- Do not overmix the batter. If you overmix batter you’ll end up with muffins that are more dense and gummy instead of fluffy and soft. Plus, you want to be careful not to “over-swirl” the batters together.
- Use fresh baking soda. If your baking soda is older than 3 months, I suggest grabbing a new one for best baking results.
How to “marble” these chocolate pumpkin muffins
There are a few simple tips & tricks I have for creating that beautiful “marble” effect in these chocolate pumpkin muffins. Here’s how to do it:
- Start by making one batter, then divide it evenly into two bowls and add a little cocoa powder to one of the batters.
- Next, alternate adding the two different batters to each of your muffin liners.
- Use a knife to swirl the batter just a few times. Don’t overdo it or your batter will look all mixed together. We want to keep them pretty.
- Before baking, don’t forget to top them with a few chocolate chips if you know what’s good.
Turn these muffins into chocolate pumpkin bread
You can easily use this chocolate pumpkin muffins recipe for making a bread instead! Just layer the batter in a greased 8×4 inch loaf pan. Bake for 45-55 minutes or until tester comes out clean or with just a few crumbs attached. Alternatively, you can try my Coconut Double Chocolate Pumpkin Bread.
Freezer-friendly chocolate pumpkin muffins
These healthy marbled chocolate pumpkin muffins are freezer-friendly! Simply wrap muffins individually in freezer-safe bags or store them in a large freezer bag. When you’re ready to enjoy them, reheat them for 30-45 seconds in the microwave or simply thaw them at room temperature.
Bake them up. They’ll be glorious, I promise.
SO DAMN GLORIOUS.
More pumpkin recipes you’ll love
- Pumpkin Chocolate Chip Muffins
- Healthy Pumpkin Pancakes
- Slow Cooker Black Bean Pumpkin Turkey Chili
- Healthy Pumpkin Bread with Maple Glaze
- Pumpkin Zucchini Muffins with Cinnamon Cream Cheese Frosting
Get all of my pumpkin recipes here!
I hope you love these healthy marbled chocolate pumpkin muffins! If you make them be sure to leave a comment & a rating so I know how you liked them. Enjoy, xo!
Healthy Marbled Chocolate Pumpkin Muffins
Ingredients
- 1 cup pumpkin puree
- 1/2 cup pure maple syrup
- 2 large eggs, at room temperature
- 1/4 cup unsweetened almond milk (or milk of choice)
- 1 teaspoon vanilla extract
- 1 1/2 cups whole wheat pastry flour
- 1 teaspoon baking soda
- 1 teaspoon cinnamon
- 1/2 teaspoon nutmeg
- 1/2 teaspoon ground ginger
- 1/4 teaspoon allspice
- 1/2 teaspoon salt
- 1/4 cup coconut oil, melted and cooled (or sub melted butter or vegan butter)
- 1/4 cup unsweetened cocoa powder
- 1/2 cup chocolate chips, divided
Instructions
- Preheat oven to 350 degrees F. Line a 12 cup muffin tin with liners and spray the inside of the liners with nonstick cooking spray.
- In a large bowl, mix together pumpkin, maple syrup, eggs, almond milk and vanilla extract.
- In a separate large bowl, whisk together the dry ingredients: whole wheat pastry flour, baking soda, cinnamon, nutmeg, ginger, allspice and salt.
- Add dry ingredients to wet ingredients and mix until just combined. Next, stir in melted coconut oil.
- Divide batter in half; adding half of the batter to a seperate medium bowl. Stir in cocoa powder and ¼ cup chocolate chips into one of the batters, mixing until just combined.
- First spoon a less less than 1 tablespoon of the pumpkin batter into each muffin liner and then spoon 1 tablespoon chocolate batter on top. Repeat until all of your muffin batter is gone.
- Swirl the batters together with a knife, just about 3-4 times. Don’t go crazy or the batter won’t look nice and swirled.
- Gently shake your muffin pan back and forth just a few times to even out the batter. Top batter with remaining chocolate chips.
- Bake for 20-25 minutes until a tester comes out clean. Mine were perfect at 22 minutes. Cool in pan for 10 minutes, then transfer to a wire rack to finish cooling.
Recipe Notes
Nutrition
148 comments
Love this beautiful and fun presentation!! 🙂
Love this beautiful and fun presentation!! 🙂
Thank you! They were fun to make 🙂
I can’t pin any of your recipes. Is anyone else having this problem? It’s fine on other sites. Help!These look amazing.
Hi Lori! We’re looking into the pinning issue – apologies for any inconvenience. For now feel free to pin this recipe by clicking here!
Yes, I have been having this issue, too!
It should be working now!
I can’t pin any of your recipes. Is anyone else having this problem? It’s fine on other sites. Help!These look amazing.
Hi Lori! We’re looking into the pinning issue – apologies for any inconvenience. For now feel free to pin this recipe by clicking here!
Yes, I have been having this issue, too!
It should be working now!
GIRL! I made these yesterday (with butter because I didn’t have coconut oil) and they are awesome!
GIRL! I made these yesterday (with butter because I didn’t have coconut oil) and they are awesome!
YES so happy to hear that!
These are so beautiful! And on top of that, I’m sure delicious! They seem perfect for this season.
These are so beautiful! And on top of that, I’m sure delicious! They seem perfect for this season.
Absolutely! They’re a great snack or healthy treat.
YES, PUMPKIN WEEK! I am ALL about pumpkin. Kabocha squash, pumpkin puree for baking, pumpkin soup, pumpkin curry, pumpkin pancakes, and so much more. These muffins look absolutely glorious with the rich chocolate aspect of the batch. Chocolate chips on top too? WINNING. If I do make this recipe, I’ll be sure to sub the eggs for flax eggs!
Loving all things pumpkin over here! Hope you get a chance to make these Cassie 🙂
Can i use all purpose flour if I don’t have pastry flour?
Yes, that should work!
I sifted together whole wheat and AP flour and sifted. Great texture.
Perfect!
I can’t seem to pin any of your posts anymore. I keep getting messages that “This site doesn’t allow you to save Pins.” I’ve tried various methods (browser button, Save icon on pictures, going straight through Pinterest…) with the same result.
I can’t seem to pin any of your posts anymore. I keep getting messages that “This site doesn’t allow you to save Pins.” I’ve tried various methods (browser button, Save icon on pictures, going straight through Pinterest…) with the same result.
It should be fixed now!
It is! Thank you! 🙂
what can replace eggs for vegan option?
Hi! The notes section of the recipe tells you how to make these vegan.
you didnt put a measurement for cloves so i assumed it was the same as the allspice !!! i am so excited to taste these suckers they smell amazing
update – they didn’t even last two days and my kids are asking for round 2! My new fav pumpkin recipe by far
Amazing!! So happy to hear that, Brit.
you didnt put a measurement for cloves so i assumed it was the same as the allspice !!! i am so excited to taste these suckers they smell amazing
update – they didn’t even last two days and my kids are asking for round 2! My new fav pumpkin recipe by far
Amazing!! So happy to hear that, Brit.
How do you think spelt flour would fair in this recipe? Drooling.
How do you think spelt flour would fair in this recipe? Drooling.
Spelt flour will work wonderfully.
Hi! Could I substitute the flour with whole wheat pastry flour instead? Thanks!
Hi! Could I substitute the flour with whole wheat pastry flour instead? Thanks!
Hi, so sorry. Promise I read good! lol I answered my own question. Just needed to read 😜
No problem! 😉
Hi, so sorry. Promise I read good! lol I answered my own question. Just needed to read 😜
No problem! 😉
Cannot wait to try these! Would it be ok to substitute olive oil or vegetable oil instead of the coconut oil?
Yes, definitely — both will work but I recommend a light olive oil.
Cannot wait to try these! Would it be ok to substitute olive oil or vegetable oil instead of the coconut oil?
Yes, definitely — both will work but I recommend a light olive oil.
Had to sub the maple syrup for honey and pumpkin pie spice instead of all the non-cinnamon spices but they still turned out AMAZING! So puffy and round with a perfect texture/crumb. Not too sweet and the pumpkin and chocolate balance each other nicely! I’ll definitely make them again.
Perfect! So happy you liked them!
Can this be made into a loaf instead? How should it be modified? Thanks!
Yep! There are instructions in the “Notes” section 🙂 Just layer the batter in a greased 8×4 inch loaf pan. Bake for 45-55 minutes or until tester comes out clean or with just a few crumbs attached.
Can this be made into a loaf instead? How should it be modified? Thanks!
Yep! There are instructions in the “Notes” section 🙂 Just layer the batter in a greased 8×4 inch loaf pan. Bake for 45-55 minutes or until tester comes out clean or with just a few crumbs attached.
These are so amazing! A family hit!!I used whole spelt (I often use for breads and muffins). They were fluffy yet moist, just the right amount of sweet!
Amazing! Glad everyone loved them 🙂
Awesome! I was looking for a cupcake recipe for my daughter’s 5 year birthday in October, and thought pumpkin would be cool, and found this! Cannot WAIT to try it !!!
Perfect!! Hope you both love these <3
I’ve made these 4 times already! Used Bob’s Red Mill GF flour blend… turned out great! Thank you!
I’ve made these 4 times already! Used Bob’s Red Mill GF flour blend… turned out great! Thank you!
Perfect!!
Hi Monique (fellow neighbor) ! I am writing from the coldest day ever in Chicago and looking up yummy recipes while my daughter watches Frozen 😉 Is the pumpkin puree from a can (same thing as a canned pumpkin?) Also, if I don’t have whole wheat pastry flour, can I use white whole wheat flour instead? Thank you!!! Stay warm and safe!
Hi Monique (fellow neighbor) ! I am writing from the coldest day ever in Chicago and looking up yummy recipes while my daughter watches Frozen 😉 Is the pumpkin puree from a can (same thing as a canned pumpkin?) Also, if I don’t have whole wheat pastry flour, can I use white whole wheat flour instead? Thank you!!! Stay warm and safe!
I made this recipe. I sub maple for date paste. The are amazing. 5 star ⭐️ rating.
Great! I’m glad the date paste worked out. Glad you enjoyed!
What is the measurement of pumpkin purée for this recipe? I’d like to use homemade purée but need to know what the ‘can’ amount is. Thank you
Hi Nicki! In the ingredients you’ll find the exact measurement – just 1 cup of pumpkin purée.
Hello Monique,
I was wondering if you could sub the whole wheat flour with quinoa flour? Would that still work?
Hi Stephanie! I haven’t tried it, but I think it would work. I might suggest making sure the quinoa flour is toasted first before using in the recipe to remove any bitterness. 🙂
Looks delicious!! If I am using almond flour, how much would the recipe call for?
Thanks and Happy Autumn!!
Hi Andrea! I wouldn’t suggest using almond flour in this one – check out the notes section of the recipe for a couple of gluten free options 🙂
Enjoy!
Hi dear , can I use coconut flour in this recipe
Hi! I wouldn’t recommend it in this recipe. Feel free to check the notes section for my suggested gluten free substitutions 🙂
The Muffin Queen does it again! I made these this morning and they turned out great. I would’ve liked them to be a tiny bit sweeter, but that’s a personal preference. They were a bit difficult to swirl, as the chocolate dough was really sticky. But, I did my best and they’re delicious anyway! 🙂 Thanks for another great recipe!
Glad you enjoyed! Feel free to add a bit more chocolate chips next time, too 🙂
Your recipes have become some of our very favorite recipes- thank you! Is there a way to use oat flour or a oat and almond flour blend? We don’t have any gluten free flour you recommend on hand.
So happy to hear that! I haven’t tried it, but I think it would change the texture significantly, so I probably wouldn’t recommend, sorry!
The batter seemed a bit thick post coconut oil, but I think it was because I used regular Whole Wheat flour instead of Whole Wheat Pastry. I used 1 egg + 1 flax egg and cut the maple syrup in half and used 1/4C apple sauce.. Also, next time I definitely should more precisely cut the batter in half because the cocoa powder sucked the moisture out of the one half, I add an additional tbsp of pumpkin and ~2tbsp of oat milk. I was worried that they’d come out too dry, but they are AMAZING and perfect at 22 minutes. Going to make again and swirl the muffins a bit more.
Those little changes are likely what made the batter thicker, but I’m glad they turned out well!
Very good flavor. I found that splitting the batter in half, then adding the cocoa, made for too much chocolate and not enough pumpkin. I think I will make slightly less chocolate batter next time. I used regular whole wheat flour and they were still tender.
Glad you enjoyed! Let me know how it goes with less chocolate.
So delicious and the perfect amount of sweetness! I’ll be making these again!
Absolutely! Glad you loved them!
This is one of my favourite pumpkin muffin recipes ever! The combination of pumpkin, chocolate, and pumpkin spices is so good!!! Made this vegan by using flax eggs and it turned out great 🙂
Amazing! One of my favs, too 🙂 glad the flax eggs work out well!
Simply amazing! Great texture, amazing flavor and the marbling effect makes them look professionally made! I substituted 1/4 cup of the flour with 1/4 cup of protein powder just to make it even healthier and it turned out great. You’d never noticed.
Perfect! Glad the protein powder worked out well 🙂
Delicious!
One of my favorites 🙂
Made this according to the recipe except used regular unbleached organic flour and extra creamy oat milk. They turned out fantastic and both my son & I love them. We are pumpkin people and I especially liked that they are not super sweet, but so gooey with the chocolate chips! They are also really pretty, a great muffin to take to a special event. Thank you for this awesome recipe.
Perfect! So happy to hear that 🙂
Loved this recipe ! The marble look was just beautiful. Not to sweet either. I was big hit in our family.
Needing no mixer was a plus.
Thinking of making these, but I don’t have pastry flour. Can I sub regular all purpose flour? If yes, would it still be the same ratio?
These are delicious! They were easy to make and have the perfect balance of chocolate and pumpkin. They also came out so beautifully!
The perfect flavor combo! Glad you enjoyed 🙂
I make these several times every fall because 1. the chocolate & pumpkin spice combo is amazing and 2. they are so fun to make! I was worried that I way overmixed them this time but they still turned out perfectly soft, fluffy and moist.
So good!! Glad they’re a favorite, Molly 🙂
Wonderful recipe – I subbed 100% whole wheat stone ground flour which resulted in a denser muffin, but the taste is spot on! Not too sweet and perfectly pumpkin-y!
Whole wheat flour does tend to bake up denser but I’m glad you liked them regardless!
These muffins are moist and delicious! I will definitely make these again.
I made a double batch of these and have been eating them all week with hubby for breakfast. Delicious! I experimented and cut down the maple to 1/3 cup to limit the sugar and sweetness. Definitely less sweet, so if anyone likes sweet muffins I would do all the recommended maple.. I’ve never made a marbled muffin, but your instructions were easy and they came out beautifully!
Perfect! So glad you enjoyed 🙂
Have made this several times. Am about to make it a bread loaf for the first time. So yummy and I love anything pumpkin!
Perfect! Hope you love the loaf!
These muffins are quite possibly my favorite pumpkin treat. They are truly the best of both worlds with fudgy chocolate, cozy pumpkin and warm fall spices. My chocolate batter was kind of thick after adding the cocoa powder but they baked up perfectly.
Muffins were great, no added sugar sl not super sweet which is perfect for my taste!
The perfect snack or breakfast!
Loved this recipe! Super simple to make. I made it as a bread and served it with some almond butter on top. So yummy!
Love that! Glad you enjoyed 🙂
Hey, there! Could I use pumpkin pie spice to replace the other spices (I don’t have allspice). If so, how much would you use? Thanks!
Hi! Yep 🙂 you can use about 1 1/4 teaspoons.
Great way to use up 1 cup of canned pumpkin 🙂 These were NOT too sweet – perfect for some, maybe not sweet enough for others. I used high cocoa chocolate chunks. Next time I might use sweeter chocolate. Even the pumpkin batter wasn’t overly sweet. The batter was quite thick so I couldn’t really ‘marble’ it, but having the chocolate batter on top of the pumpkin batter was still a lovely look.
Absolutely! And yes I’d recommend a sweeter chocolate if you prefer them to be a bit sweeter 🙂
Made this twice over the last month and the family loves it! Made it as a loaf instead of muffins and baked for 55-60 minutes. Similar to another comment, I added an extra tablespoon or so more of pumpkin purée and a splash of almond milk to the cocoa mixture to make it smoother. This recipe is now a go-to favourite.
Perfect! I’m glad the loaf worked out well 🙂
This recipe is amazing! Hands down my favorite muffin recipe. Such a great blend of pumpkin & chocolate!
So happy to hear that! Favs for fall.
We usually always have one baked good on the table and I had a bag of cocoa powder I hadn’t gone through so I decided to make a loaf of this marbled pumpkin recipe. I don’t like overly sweet stuff and this recipe was just right despite the maple syrup. I didn’t add choco chips so that might add some more sweetness and moisture. Overall such a great hit that balanced nicely with my mid day tea and morning coffee.
Perfect! So happy you gave this one a try 🙂
Yummy and easy to make. I made it in a bread form and it came out great.
Perfect! So happy to hear that 🙂
I love these muffins! I made them for the first time in the fall and they were so good I keep making them year-round and they are my favorite breakfast with some coffee! I usually sub in 2% milk, all-purpose flour, and melted butter, and I sometimes use pumpkin pie spice instead of the individual spices. I also usually make a double batch and freeze them. One of my favorite recipes!
OK can I just say these are.. DELICIOUS!! They aren’t too sweet, but you still taste that chocolate-ly, pumpkin goodness. I’ve made these twice and they’ve been eaten so quick! 🙂
I replaced the pumpkin with applesauce, skipped all the spices (instead of salt) and ended up with some really really rich, moist, and delicious muffins! 100% would make again.
I’m glad that worked out well!
The most baked muffin in our household!! We love it.
Confession: I find it quicker and just as delicious to combine the ingredients and not have the marbled look. Just an amazing chocolate/pumpkin/spice muffin. Heat it up for a few seconds in the microwave before eating and YUM!
SO happy you guys love this one, Amy! And yes, no need to marble if you don’t want to!
Great recipe. I didn’t marble it. I added 1 more T cocoa and mixed the cocoa into all the batter. Was short on pumpkin and added enough applesauce to make the 1cup. About 2/3 pumpkin and 1/3 applesauce. Texture is fluffy. Instead of milk I used some chocolate energy drink that needed used up. About the same calorie content as milk and it worked fine.
loveee the chocolate pumpkin combo! I used half oat flour and half all purpose flour, cacao powder instead of cocoa and baked for just 20 min and they were perfect!!!! xoxox
So glad that all worked out well and that you loved them, Alanna!
So so soft, light, and fluffy! I didn’t have pastry flour available. I did a combo of whole wheat and oat flour and they were amazing! I like that you can actually taste the spice. Next time I think I’ll leave out the cocoa powder just so I can taste the pumpkin more.
So glad that worked well and that you loved them!
I tried this recipe for the first time this morning, after searching AK for a pumpkin chocolate chip muffin. I followed directions as written, except I used 2 flax eggs. They baked for 21 minutes and turned out GREAT!! The texture and taste is SO good, and with the perfect amount of sweetness.
Yay!! So happy they came out perfect and that you loved them, Laura!
Just made these for my family. They were amazing. Soft and sweet, but not too sweet or too spicy. Just perfect!
really great! I forgot to add the chocolate chips to the batter but they were still great.
Made as written. Delicious and easy!
My family loves these. We usually throw in a cup of grated, squeezed out zucchini too for extra veggies and moisture. We often double the recipe and freeze them on a sheet pan before storing in a freezer bag. They’re nice and quick for busy school mornings.
Made these with 1:1 gf flour and they are amazing!!
Yummy! How long are they food for if you freeze them?
My guess is up to 3 months!
Good morning! Any idea if this will work if made in a Bundt pan instead of as muffins? Thank you!!
Hi, there! Apologies for the delay. It should work but I haven’t tried it so I’m not completely sure!
I used applesauce instead of maple syrup, and therefore just used half the amount of milk. I also used 1/3 cup Greek yogurt instead of the 1/4 cup coconut oil.
I was going to omit the chocolate chips, but I tasted the batter and it wasn’t sweet at all, so I added about 3 chocolate chips per muffin.
They were good! My toddlers and I gobbled them up.
The recipe made about 20 for me.