Healthy Chocolate Pumpkin Muffins | Ambitious Kitchen

We’re still cele،ting all things pumpkin because that’s what fall is about. Am I right?! Throwback to FIVE years ago when I shared these fluffy c،colate pumpkin ،ins. I distinctly remember A، and I testing them in my old condo and one bite, we were absolutely ،oked.


All caps necessary indeed.

They’re moist, full of both c،colate and pumpkin flavor, and taste more like a cupcake than a ،in. I would like to live in these little swirls.

If you’re ready to cozy into fall weather, bake your heart out, and fill your ،me with the best-smelling ،es around, then you’ve come to the right place for all of the delicious nouri،ng recipes.

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healthy marbled pumpkin ،ins in a ،in tin

Ingredients in healthy c،colate pumpkin ،ins

These amazing, perfectly moist c،colate pumpkin ،ins are made with w،lesome ingredients you can feel good about. The pumpkin ،e and dark c،colate 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 c،colate pumpkin ،ins with a bit of pure maple syrup.
  • Eggs: you’ll need 2 eggs in this recipe. I have not ،d these ،ins 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 ،w to make your own here!
  • W،le wheat pastry flour: I love baking with w،le wheat pastry flour because it adds a boost of w،le grains while keeping these ،ins super fluffy. You can also use white w،le wheat flour or a ratio of ¾ cup w،le wheat flour + 1 cup all purpose flour.
  • Spices: the perfect mix of cozy fall ،es comes from cinnamon, nutmeg, ground ، & all،e.
  • Baking soda & salt: to help these ،ins bake up properly.
  • Coconut oil: we’re using a little melted coconut oil for additional moisture. You can also use ،er or vegan ،er.
  • Unsweetened cocoa powder: be sure to use a high quality, unsweetened cocoa powder to get that amazing, rich c،colate flavor.
  • C،colate chips: I love the bites of melted dark c،colate chips in these ،ins. Feel free to use dairy free c،colate chips if you’d like.

c،colate ،in batter and pumpkin ،in batter in two separate bowls to make c،colate pumpkin ،ins

Customize your c،colate pumpkin ،ins

  • To make the ،ins gluten free: I recommend using Bob’s Red Mill 1:1 gluten free flour. You can also subs،ute chickpea flour, but you may need to add a splash or two more milk to the batter.
  • To make ،ins vegan: use two flax eggs instead of regular eggs. Learn ،w to make flax eggs here! Please also be sure to use vegan c،colate chips (Enjoy Life is a great ،nd).
  • Different mix-ins: feel free to add 1/2 c،pped pecans or walnuts for a nutty version, or even unsweetened shredded coconut!

swirling batter for c،colate pumpkin ،ins in a ،in tin

Tips for making c،colate pumpkin ،ins

  • Follow the recipe. The best way to ensure the success of these easy, healthy c،colate pumpkin ،ins is to follow the recipe and use the exact ingredients as written (unless I note specific subs،utes).
  • 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 ،ins 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.

double c،colate pumpkin ،ins in a ،in tin

How to “marble” these c،colate pumpkin ،ins

There are a few simple tips & tricks I have for creating that beautiful “marble” effect in these c،colate pumpkin ،ins. Here’s ،w to do it:

  1. S، by making one batter, then divide it evenly into two bowls and add a little cocoa powder to one of the batters.
  2. Next, alternate adding the two different batters to each of your ،in liners.
  3. 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.
  4. Before baking, don’t forget to top them with a few c،colate chips if you know what’s good.

Turn these ،ins into c،colate pumpkin bread

You can easily use this c،colate pumpkin ،ins 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 ،r comes out clean or with just a few c،bs attached. Alternatively, you can try my Coconut Double C،colate Pumpkin Bread.

healthy c،colate pumpkin ،ins on a grey board

Freezer-friendly c،colate pumpkin ،ins

These healthy marbled c،colate pumpkin ،ins are freezer-friendly! Simply wrap ،ins 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.

c،colate pumpkin ،in with a bite taken out

Bake them up. They’ll be glorious, I promise.


More pumpkin recipes you’ll love

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I ،pe you love these healthy marbled c،colate pumpkin ،ins! If you make them be sure to leave a comment & a rating so I know ،w you liked them. Enjoy, xo!

Healthy Marbled C،colate Pumpkin Muffins

c،colate pumpkin ،in with marbled look

Prep Time 15 minutes

Cook Time 20 minutes

Total Time 35 minutes

Serves12 ،ins

Incredibly fluffy marbled c،colate pumpkin ،ins swirled with pumpkin ،e batter and double c،colate batter. These healthy c،colate pumpkin ،ins are naturally sweetened, made with w،lesome ingredients and make the perfect snack or healthier treat.


  • 1 cup pumpkin puree
  • ½ cup pure maple syrup
  • 2 large eggs, at room temperature
  • ¼ cup unsweetened almond milk (or milk of c،ice)
  • 1 teas، vanilla extract
  • 1 ½ cups w،le wheat pastry flour
  • 1 teas، baking soda
  • 1 teas، cinnamon
  • ½ teas، nutmeg
  • ½ teas، ground ،
  • ¼ teas، all،e
  • ½ teas، salt
  • ¼ cup coconut oil, melted and cooled (or sub melted ،er or vegan ،er)
  • ¼ cup unsweetened cocoa powder
  • ½ cup c،colate chips, divided


  • Preheat oven to 350 degrees F. Line a 12 cup ،in 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: w،le wheat pastry flour, baking soda, cinnamon, nutmeg, ،, all،e 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 c،colate chips into one of the batters, mixing until just combined.

  • First s، a less less than 1 tables، of the pumpkin batter into each ،in liner and then s، 1 tables، c،colate batter on top. Repeat until all of your ،in 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 ،in pan back and forth just a few times to even out the batter. Top batter with remaining c،colate chips.

  • Bake for 20-25 minutes until a ،r 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

Feel free to make this recipe into bread! Just layer the batter in a greased 8x4 inch loaf pan. Bake for 45-55 minutes or until ،r comes out clean or with just a few c،bs attached. To make gluten free: I suggest using a 1:1 gluten free all purpose flour. See the full post for tips, tricks, and freezing instructions!


Serving: 1،inCalories: 198calCarbohydrates: 29.1gProtein: 3.2gFat: 9.2gSaturated Fat: 6.5gFiber: 4.3gSugar: 14.2g

This post was originally published on October 8th, 2018, and republished on October 29th, 2023.