Throwback to FIVE years ago when I shared these fluffy chocolate pumpkin muffins. I distinctly remember Abra and I testing them in my old condo, and one bite, we were absolutely hooked.
In fact, THEY MIGHT JUST BE THE BEST MUFFINS I’VE EVER MADE.
They’re moist, full of both chocolate and pumpkin flavor, and taste more like a cupcake than a muffin. I would like to live in these little swirls. It’s time to bake our hearts out and start cozying into fall.
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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.
- Milk: a bit of milk adds the perfect amount of moisture. I like to use unsweetened almond milk, but feel free to use any milk you’d like.
- Baking staples: you’ll also need vanilla extract, baking soda, and salt.
- 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.
- 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.
Customize your muffins
- To make the muffins gluten-free: I recommend using a 1:1 gluten-free all purpose 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 dairy-free chocolate chips.
- Different mix-ins: feel free to add 1/2 cup chopped pecans or walnuts for a nutty version, or even unsweetened shredded coconut!
Don’t forget these muffin-baking tips
- 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).
- Use room temp eggs. If your eggs are too cold, you risk the coconut oil coagulating. To bring your eggs to room temperature, 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 the batter, you’ll end up with muffins that are denser 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 recipe to make a bread instead! Just layer the batter in a greased 8×4 inch loaf pan. Bake for 45-55 minutes or until a tester comes out clean or with just a few crumbs attached. Alternatively, you can try my Coconut Double Chocolate Pumpkin Bread.
Want to make mini muffins?
It’s so easy! I love making these mini for my kids. Here’s how:
- Pour the batter into a mini muffin pan with mini muffin liners.
- Bake at 400 degrees F for 9 to 14 minutes! Mine are usually perfect around 12 minutes.
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.
Our favorite muffin-baking tools
- Kitchen scale
- Mixing bowls
- Wooden spoon
- Whisk
- Muffin pan
- Muffin liners
- Nonstick cooking spray
- Wire rack
Get all of my kitchen essentials here!
More pumpkin recipes you’ll love
- Healthy Pumpkin Pancakes
- Outrageously Good Pumpkin Protein Muffins
- Healthy Pumpkin Bread with Maple Glaze
- Marbled Pumpkin Snacking Cake (gluten free!)
- Vegetarian Spinach Pumpkin Lasagna
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!
Ambitious Kitchen
Cookbook
125 Ridiculously Good For You, Sometimes Indulgent, and Absolutely Never Boring Recipes for Every Meal of the Day
Healthy Marbled Chocolate Pumpkin Muffins
Ingredients
- 1 cup (244 grams) pumpkin puree
- ½ cup (156 grams) pure maple syrup
- 2 large eggs, at room temperature
- ¼ cup (60 grams) unsweetened almond milk (or milk of choice)
- 1 teaspoon vanilla extract
- 1 ½ cups (170 grams) whole wheat pastry flour
- 1 teaspoon baking soda
- 1 teaspoon cinnamon
- ½ teaspoon nutmeg
- ½ teaspoon ground ginger
- ¼ teaspoon allspice
- ½ teaspoon salt
- ¼ cup (56 grams) coconut oil, melted and cooled (or sub melted butter or vegan butter)
- ¼ cup (20 grams) unsweetened cocoa powder
- ½ cup (90 grams) 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 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
This post was originally published on October 8th, 2018, republished on October 29th, 2023, and republished September 10th, 2026.
delish. new favorite
I’m so glad!!
Would it be possible to substitute almond flour in this recipe?
I haven’t tested these with almond flour, so I can’t recommend it!
Did you try it with almond flour? If so, what measurements and how did it come out?
These are so good that I made them twice in one week!
So glad you loved them!
So good! I didn’t add the cocoa powder but still great recipe and perfect sweetness👌🏻
Perfect! Glad you enjoyed!
A family favorite! Everyone loves these. They are super easy to make too. Thank you!
So happy to hear that!
These were good like a 3.5/5, but dry and lacked sweetness (and we don’t like overly sweet treats for context). I think I’d swap the coconut oil with applesauce and see if that solves the sweetness issue and go from there in gauging if the batter seems moist enough.
Sorry that you didn’t love these! Let me know how it goes with applesauce.
These are fantastic. I love that they are not overly sweet! Perfect fall treat! I will be making these again!!!
Absolutely! Glad you enjoyed!
I love these muffins yet my batter wasn’t liquidy enough to swirl the batter to create a marble effect. It was more dry when i would scoop the batter 🙁
I followed the directions exactly and let the coconut oil cool before adding to my mix.
Any ideas?
So strange! Did you make sure to use the spoon and level method to measure the flour? It sounds like there could’ve been too much flour or a dry ingredient. Otherwise, you could add a bit more milk to help loosen the batter.
Not sweet at all, and I’m not even a fan of super sweet desserts. Followed the recipe EXACTLY (even splitting the batter in half using weight measurements to ensure it was exact). Honestly inedible unless you make some type of sweet frosting
Sorry to hear that! With the 1/2 cup of maple syrup and the chocolate chips I’ve always found these to be perfectly sweet, so I’m not sure what could’ve gone wrong here.
These turned out great. Just sweet enough for it to be a treat but not overly sweet. 4 year old approved!
So happy to hear that!
Made these with my own gf flour blend and they are delicious! Also used butter rather than coconut oil and that was a great substitute as well.
Perfect! Glad the GF flour worked out well.
Absolutely delicious. Muffins were perfectly moist at 19 mins. Thanks for the great recipes.
So happy to hear that!
My super picky daughter says these are the best muffins ever. After I popped them in the oven and tasted the batter, I thought there’s no way she’ll even eat these, not sweet enough. But I was wrong! They’re the perfect balance of flavours. They’re really pretty too.
WOO! this is seriously the best, glad these are a hit for everyone!
Is it possible to swap the whole wheat flour with a 1:1 gluten free flour? This sounds amazing but I can’t do gluten.
Hi! Yes! Bob’s Red Mill 1:1 GF flour is my favorite.
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.
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!
Yummy! How long are they food for if you freeze them?
My guess is up to 3 months!
Made these with 1:1 gf flour and they are amazing!!
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 as written. Delicious and easy!
really great! I forgot to add the chocolate chips to the batter but they were still great.
Just made these for my family. They were amazing. Soft and sweet, but not too sweet or too spicy. Just perfect!
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!
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!
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!
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.
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!
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!
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 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!
Yummy and easy to make. I made it in a bread form and it came out great.
Perfect! So happy to hear that 🙂
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 🙂