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These Chocolate Chip Butternut Squash Muffins are made with bananas, squash, and whole-grain oats. They bake up tender, delicious, and full of flavor. They’re a healthy, gluten-free treat everyone loves!

I’ve fallen in love with a new muffin. Chocolate Chip Muffins with Butternut Squash! Butternut squash is one of my favorite ingredients in the fall. I make my roasted butternut salad on repeat! And I knew when I tasted the batter they were gonna be terribly good. They’re wholesome and hearty you don’t even know they have a veggie stashed in them. Sneaky.
I’m not sure I could ever pick a favorite muffin although banana bread muffins still have a piece of my heart. I guess I can have multiple loves, but for right now these Chocolate Chip Butternut Squash Muffins are my love muffins. Hope you love it!
Table of Contents
Why You Will Love Butternut Squash Chocolate Chip Muffins
- Healthy Muffins. The main ingredient in this muffin recipe is butternut squash which is high in vitamin A, vitamin C, magnesium, and potassium. These muffins are also dairy-free, gluten-free, and nut-free.
- Quick and Easy to Make: Mixing the muffins takes just minutes of active time.
- Versatile Baked Good: Enjoy these muffins for breakfast, brunch, or as a healthy butternut squash dessert.
Ingredients
Let’s take a look at the main ingredients you will need to gather to make these gluten-free muffins with butternut squash and chocolate chips.

- Bananas: For best results make sure they are very ripe. The riper the bananas the more sweetness they add as well they’re easier to mash.
- Butternut squash puree: I use canned squash puree to save time but you can make your own my cooking butternut squash and mashing it.
- Egg whites: I like using egg whites as the binder for this easy recipe. You can also use a whole egg if you prefer.
- Maple syrup: Adds a bit of sweetness that’s less processed than using granulated sugar.
- Spices: These chocolate chip butternut squash muffins are flavored with cinnamon, ginger, and nutmeg.
- Baking soda: Gives your blender muffins a bit of lift.
- Flour: This recipe uses a combination of gluten-free baking flour such as the 1-to-1 flour by Bob’s Red Mill and gluten-free oat flour.
- Rolled Oats: Make sure you choose gluten-free oats as not all oatmeal is gluten-free.
- Mini chocolate chips: Choose non-dairy chocolate chips such as Enjoy Life to keep this recipe dairy-free.

How to Make Butternut Squash Muffins
Mixing these muffins takes just minutes. Here’s a look at the main steps you will take to make them. Be sure to check the recipe card for the full details.
- Combine the bananas, egg whites, coconut oil, maple syrup, and butternut squash in a food processor or blender. Process or blend until the wet ingredients are smooth.
- Add both types of flour, cinnamon, ginger, nutmeg, and salt to the food processor or blender. Process again until the mixture is smooth.


- Transfer the ingredients to a mixing bowl. Add the oats and chocolate chips to the bowl and fold them into the batter.
- Spoon the batter into the muffin pan openings filling each only three-quarters full.


- Bake the muffins for 15 minutes. Remove the pan from the oven and cool for 5 minutes in the pan. Transfer the muffins to a baking rack to finish cooling.

How to Store
- Store: Store your baked muffins in an airtight container in the fridge for up to a week. If you want to enjoy it warm, you can pop it in the microwave for a few seconds.
- Freeze: To extend their shelf-life place them in a freezer-safe container and store them for up to two months.
Expert Tips
- Transfer your muffins to a cooling rack after cooling for five minutes in the pan after removing them from the oven. This will prevent tough or overcooked muffins.
- Don’t like chocolate chips? You can swap them for dried cranberries or raisins instead.
- Use muffin liners or spray your pan well. Both of these options are ideal to prevent sticking.
- Sprinkle some chocolate chips on top of the muffins right before baking if you want the chocolate chips more visible.
- Make sure you measure your flour properly to avoid tough or dry muffins.
Recipe FAQs
If you don’t need them to be gluten-free you can swap the 1-to-1 flour for regular all-purpose flour but I don’t recommend mixing it in the blender. Instead after blending the bananas and butternut squash, transfer the mixture to a mixing bowl and stir in the flour by hand. This will prevent over-activating the gluten in the flour which may make these muffins tough.
This butternut squash muffin recipe works great with pumpkin or you can also use acorn squash or buttercup squash instead.

More Gluten-Free Muffin Recipes
If you tried this Butternut Squash Muffins or any other recipe on my website, please please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

Healthy Butternut Squash Muffins with Chocolate Chips
Ingredients
- 2 bananas, very ripe, mashed
- ½ cup butternut squash puree
- 2 egg whites
- ½ cup coconut oil, melted
- ½ cup maple syrup
- ½ teaspoon cinnamon
- ¼ teaspoon ginger
- ⅛ teaspoon nutmeg
- ½ teaspoon sea salt
- 1 teaspoon baking soda
- 1 cup Gluten Free 1:1 Baking Flour
- ⅔ cup Gluten Free Oat Flour
- ¾ cup Gluten Free Rolled Oats
- ½ cup mini chocolate chips, or dairy free chocolate chips
Instructions
- Preheat oven 375 F. Prepare a muffin tin with cooking spray.
- In a food processor or blender, add bananas, egg whites, coconut oil, maple syrup and butternut squash. Process until wet ingredients are smooth.
- Next add the 2 flours, cinnamon, ginger, nutmeg and salt to the food processor or blender. Process until smooth.
- Transfer the ingredients to a mixing bowl. Add the oats and chocolate chips and fold into the batter.
- Spoon the batter into the muffin cavities 3/4 of the way full.
- Bake 15 minutes. Remove from the oven and cool in the pan 5 minute before transferring to a baking rack to cool another 15 minutes before eating.
- Store muffins in the refrigerator up to 1 week or freezer up to 60 days.
Notes
- My Amazon shop has more products similar to those used for this recipe and that I recommend to my nutrition clients.
- Transfer your muffins to a cooling rack after cooling for five minutes in the pan after removing them from the oven. This will prevent tough or overcooked muffins.
- Don’t like chocolate chips? You can swap them for dried cranberries or raisins instead.
- Use muffin liners or spray your pan well. Both of these options are ideal to prevent sticking.
- Sprinkle some chocolate chips on top of the muffins right before baking if you want the chocolate chips more visible.
- Make sure you measure your flour properly to avoid tough or dry muffins.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Just playing catch up this weekend- These look amazing and your photos are beautiful- How did you know I have leftover butternut squash?! Pinned to make next week!
Thanks Arman!
I’m visiting from the Pretty Pintastic Link-Up! This is definitely a first–squash in a muffin, but they look worth trying! 🙂 I hope your week looks up!
They are unique. Glad you enjoyed them!
Butternut squash in these?! WOW! They look phenomenal! Thanks for joining us at the #HomeMattersParty – we hope to see you again next week! Feel free to bring a friend with you 🙂 Happy Friday! #TGIF
Thanks, Kristen!
have you ever tried subbing the whole wheat flour with coconut flour or do you think that would work just as well??
these look so good!! 🙂
I have not used coconut flour. I suspect it may not stand up well as it absorbs liquid very quickly. Almond or oat flour may do much better.
I love adding random veggies to my baked goods. Definitely have to try this! Pinned 😀
Yay, enjoy!
I WANT IN ON THIS!!!!!! Butternut Squash completes me!
Of course you do!!! I wouldn’t expect less from you 🙂
Mmmm…butternut squash sounds absolutely delicious in these! Life can be absolutely frustrating sometimes, and I’m so sorry about all it’s throwing at you right now! Good news…these muffins are amazing!! Pinned!
Hope you like them Anna!
I’ve never tried butternut squash in a muffin, these look soo moist and amazing though! I am craving muffins now!! 🙂
They’re really moist, but hearty with the whole wheat flour and oats. Hope you enjoy them!
Oh, I do feel for you with the medical bills. I understand your frustration as well, misdiagnosis’ happen all the time and it’s simply wrong for them to charge when they didn’t even help in the first place! My father has been going through so many medical problems and tests with his cancer and the medical bills have been piling up. Our health care system is SO messed up.
I will be thinking about you and your health! Wishing you the best! Also…kudos for adding butternut squash to muffins. I like it when people do crazy recipes like this!
Thanks Kaylin, I appreciate that. I’m glad someone can relate to my frustration with health care. All the best to your father.
O hello!! Loving the combination and these look so moist and decadent! Stopping by from Treasure Box Tuesday!
Thanks Kim! I’m glad you stopped by.