These chocolate butternut squash muffins are moist and tender with a rich chocolate flavor. They're completely flourless - made with pureed butternut squash, eggs, cacao powder and almond butter. In addition, these squash muffins are gluten free, dairy free and paleo friendly.

We tried growing our own butternut squash this year, but unfortunately it was a complete failure. Our plant didn't produce a single squash!
Anyway, that won't keep me from enjoying all the winter squash this season.
While I love roasted or simple pureed squash, I also love it in the form of baked goods such as butternut squash tots, cookies, brownies and these chocolate butternut squash muffins.
These muffins are soft, moist and tender with a rich chocolate flavor. You can't taste the squash - promise! Even my kids and husband (who don't like squash) gave these chocolate squash muffins two thumbs up. In fact, I had to keep them from eating the entire batch in one sitting each time I made the recipe.
Why You'll Love these Chocolate Butternut Squash Muffins
- gluten free and grain free - these squash muffins are flourless
- paleo friendly - made with minimally processed, real food ingredients
- dairy free - no butter or milk
- easy to make - a simple, one bowl muffin recipe
- moist and soft - they have the best texture
Ingredients
Here's a list of what you'll need for these healthy chocolate squash muffins:
- pureed butternut squash
- almond butter (unsweetened, unsalted)
- eggs
- avocado oil (or another neutral oil)
- vanilla extract
- cacao powder
- coconut sugar
- baking powder
- salt
- dark chocolate chunks (or chips)
I made these butternut squash muffins with homemade squash puree, but you can use canned as well.
For the almond butter, be sure to use one that is made from just dry roasted almonds, nothing else. If it contains salt, you can omit the salt in the recipe.
I like using avocado oil in baked goods because it has a tasteless flavor and can withstand high heat. However, you can swap it for another neutral flavored oil like a light olive oil.
I prefer cacao powder to cocoa powder, as I find it less likely to dry out baked goods. I also like it's richer flavor, which may be too bitter for some people. If you use cocoa powder instead, I suggest swapping at a 1:1 ratio by weight.
Lastly, these chocolate butternut squash muffins are sweetened with coconut sugar. If you need to substitute this ingredient, make sure to swap it with another granulated sugar. Maple syrup and honey will not work in its place.
How to Make Chocolate Squash Muffins
These muffins require just one bowl, a whisk, spatula, large cookie scoop or spoon (to spoon batter into the pan), and a lined muffin pan. I recommend lining the pan with silicone baking cups because they make removal easy.
Here's what you need to do:
- First, preheat your oven to 350 degrees F. Line a muffin tin with 11 muffin liners (I used silicone).
- In a large mixing bowl, combine the wet muffin ingredients. Whisk until smooth.
- Add the dry ingredients to the wet and whisk until smooth.
- Fold the chocolate chunks into the batter.
- Use a large cookie scoop to scoop the batter into the lined muffin pan.
- Place the squash muffins in your oven and bake at 350 degrees F for 23-25 minutes.
- After baking, remove the muffins from the oven and let them cool in the baking pan for 5 minutes. Then place them on a wire cooling rack.
Storage
Since these squash muffins are moist and preservative free, I recommend storing them in the fridge. They can be kept at room temperature for a day or two, but will last longer in the fridge.
Place the muffins in a sealed, airtight container in the fridge and enjoy within one week.
Alterations for Chocolate Butternut Squash Muffins
If you're looking to switch things up, try some of these muffin alterations:
- Mix in chopped nuts or seeds
- Omit the chocolate chunks or opt for white chocolate
- Substitute the squash for pureed pumpkin or sweet potato
- Bake the muffins in a loaf pan instead (45-ish minutes)
FAQ
If you need these muffins to be nut free, swap the almond butter for sunflower seed butter. It will slightly change the taste, but they will turn out just as good!
No! No one will ever guess they're made with pureed squash!
These muffins are definitely best fresh or stored in the fridge, but you can freeze them if necessary. Cool them completely, then place them in a sealed, airtight baggie in the freezer for up to one month. When ready to eat, defrost them for 20 minutes at room temperature or at a low temp in the microwave.
More Paleo Squash Recipes
PrintChocolate Butternut Squash Muffins (Flourless)
- Prep Time: 10 minutes
- Cook Time: 23 minutes
- Total Time: 33 minutes
- Yield: 11 muffins 1x
Description
These healthy chocolate butternut squash muffins are flourless and paleo friendly. They have a rich chocolate flavor and moist, tender texture.
Ingredients
- ¾ cup butternut squash puree (175g)*
- ½ cup almond butter, unsweetened, unsalted (126g)
- 2 large eggs
- 2 Tbsp avocado oil
- ½ Tbsp vanilla extract
- ½ cup cacao powder (35g)
- ⅓ cup coconut sugar (56g)
- 2 tsp baking powder
- ¼ tsp salt
- ⅓ cup dark chocolate chunks (or chips)
Instructions
- Preheat your oven to 350 degrees F. Line a muffin tin with 11 muffin liners (I used silicone).
- In a large mixing bowl, combine the wet muffin ingredients. This includes the butternut squash, almond butter, eggs, avocado oil and vanilla. Whisk until smooth.
- Add in the cacao powder, coconut sugar, baking powder and salt. Whisk until smooth.
- Fold the chocolate chunks into the batter.
- Use a large cookie scoop to scoop the batter into the lined muffin pan, filling each slot about ¾ full.
- Place the squash muffins in your oven and bake at 350 degrees F for 23-25 minutes.
- After baking, remove the muffins from the oven and let them cool in the baking pan for 5 minutes. Then place them on a wire cooling rack.
Notes
*I steamed then pureed my own butternut squash, but you may use canned if you prefer.
Kristina
Delicious, thank you. Easy to throw together. Great texture.
Katie
Oh wonderful! So glad you enjoyed them as much as my family did 🙂 Thank you for leaving a review.
Mita C
I'm gonna make these soon. I love cooking with squash and do a few recipes like this myself!