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Home » Recipes » Breads

Butternut Squash Muffins

Published: Dec 11, 2023 · Modified: Dec 24, 2024 by Megan

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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!

A stack of butternut squash muffins with chocolate chips on top and a hand reaching to grab one.

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!

Jump to:
  • Why You Will Love Butternut Squash Chocolate Chip Muffins
  • Ingredients
  • How to Make Butternut Squash Muffins
  • How to Store
  • Expert Tips
  • Recipe FAQs
  • More Gluten-Free Muffin Recipes
  • Healthy Butternut Squash Muffins with Chocolate Chips

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.

Ingredients to make butternut squash muffins on the table before mixing.
  • 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.
A close up of butternut squash muffin with chocolate chips in a muffin pan.

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.

  1. 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.
  2. Add both types of flour, cinnamon, ginger, nutmeg, and salt to the food processor or blender. Process again until the mixture is smooth. 
Butternut squash and bananas in a blender.
Dry ingredients to make butternut squash muffins in a bowl.
  1. Transfer the ingredients to a mixing bowl. Add the oats and chocolate chips to the bowl and fold them into the batter. 
  2. Spoon the batter into the muffin pan openings filling each only three-quarters full.
Chocolate chips added to the bowl of muffin batter.
Butternut squash muffin batter scooped into a muffin tin.
  1. 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.
Butternut squash muffins with chocolate chips in a muffin pan after baking.

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

Can I make these muffins with regular flour?

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.

Can I use a different type of squash?

This butternut squash muffin recipe works great with pumpkin or you can also use acorn squash or buttercup squash instead.

Butternut squash muffins with chocolate chips on the table with a bite missing from one to show the inside texture of the muffin.

More Gluten-Free Muffin Recipes

  • Low Calorie Greek Yogurt Apple Muffins are higher protein, healthy and easy to bake!
    Low Calorie Greek Yogurt Apple Muffins
  • Low Calorie Peanut Butter Banana Muffins are a healthy muffin recipe that's higher in protein and fiber and filled with delicious, yummy flavors!
    Low Calorie Peanut Butter Banana Muffins
  • Healthy Zucchini Apple Spice Muffins are a low calorie muffin recipe made flourless with more protein and lower carbs. An easy snack recipe with warm spices! Low Calorie + Paleo + Gluten Free
    Zucchini Apple Spice Muffins {GF, Paleo, Low Cal}
  • Strawberry Greek Yogurt Muffins! Bursting with strawberries and creamy greek yogurt, these easy to make muffins make a delicious low calorie breakfast or snack for just 84 calories. Quick to make and gluten free too!
    Strawberry Greek Yogurt Muffins

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.

A butternut squash muffin on a tray with more muffins and a hand reaching to pick one up.

Healthy Butternut Squash Muffins with Chocolate Chips

Megan Olson
A simple wholesome chocolate chip muffin turned healthy. These Chocolate Chip Butternut Squash Muffins are gluten free and loved by all!
5 from 2 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 15 minutes mins
Rest Time 20 minutes mins
Total Time 45 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 15 muffins
Calories 203 kcal

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 dairy free

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

Serving: 1muffinCalories: 203kcalCarbohydrates: 27gProtein: 3gFat: 9gSaturated Fat: 7gSodium: 174mgPotassium: 137mgFiber: 2gSugar: 12gVitamin A: 520IUVitamin C: 2.3mgCalcium: 33mgIron: 0.8mg
Tried this Recipe? Let me know!Let us know how it was!

About Megan

Megan is a certified nutrition practitioner, author, freelance food photographer and fitness instructor living in Phoenix, Arizona. On her blog, Skinny Fitalicious she shares EASY, gluten free recipes for weight loss. Follow Megan on Facebook, Twitter, Pinterest and Instagram for the latest updates.

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    5 from 2 votes (2 ratings without comment)

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    Recipe Rating




  1. Andie Conn says

    March 04, 2015 at 8:12 pm

    Wow, I had no idea you could use squash in a muffin! Very creative (: Nice work.
    Visiting from http://www.andieconn.com/less-wear-spring-wardrobe-purging-closet-organization/ and would love a visit back.

    Reply
    • Megan says

      March 05, 2015 at 8:09 pm

      Zucchini's a squash and those are in many breads and muffins. Glad you liked it!

      Reply
  2. Diana Rambles says

    March 03, 2015 at 7:07 pm

    Interesting combination! I'd love to try it!

    Reply
  3. Britta says

    March 03, 2015 at 3:58 pm

    I'll bet the butternut squash makes these really moist! Your recipe is (healthy AND) wonderful and will be featured this week on Family Fun Friday Foods—the post will go live Thursday, 2pm MST on brittalafont.com. Join me there to grab your button. Thank for linking up at HappyandBlessedHome.com 🙂 Already pinned it!

    Reply
    • Megan says

      March 03, 2015 at 6:31 pm

      The muffins are to die! I love them. Hope you enjoy them too and thanks for the feature Britta!

      Reply
  4. Miz Helen says

    March 03, 2015 at 11:27 am

    We will love these muffins! Hope you are having a fantastic week and thanks so much for sharing with Full Plate Thursday.
    Come Back Soon!
    Miz Helen

    Reply
  5. Janice Wald says

    March 01, 2015 at 2:47 pm

    Hi,
    This is crazy. Only 214 calories? Get out! You are making me hungry. Chocolate chips too? Your photos look downright edible.
    Hi, I'm Janice, one of your hostesses at the Inspire Me Monday Linky party. Thank you for coming to our linky party last Monday.

    Reply
    • Megan says

      March 01, 2015 at 2:57 pm

      Sure thing, glad you liked the muffins. They're my favorite.

      Reply
  6. Arman @ thebigmansworld says

    February 28, 2015 at 7:59 pm

    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!

    Reply
    • Megan says

      March 01, 2015 at 5:42 am

      Thanks Arman!

      Reply
  7. Sharlee@mynewlines says

    February 27, 2015 at 4:05 pm

    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!

    Reply
    • Megan says

      February 27, 2015 at 4:27 pm

      They are unique. Glad you enjoyed them!

      Reply
  8. Kristen from The Road to Domestication says

    February 27, 2015 at 4:02 pm

    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

    Reply
    • Megan says

      February 27, 2015 at 4:26 pm

      Thanks, Kristen!

      Reply
  9. christine reilly says

    February 25, 2015 at 4:26 pm

    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!! 🙂

    Reply
    • Megan says

      February 25, 2015 at 4:53 pm

      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.

      Reply
  10. GiselleR @ Diary of an ExSloth says

    February 25, 2015 at 11:26 am

    I love adding random veggies to my baked goods. Definitely have to try this! Pinned 😀

    Reply
    • Megan says

      February 25, 2015 at 5:00 pm

      Yay, enjoy!

      Reply
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Megan is a nutritionist, author of the Low Calorie Cookbook and podcast host of the Dish On Ditching Diets. Megan helps women over 35 stop dieting, heal their relationship with food and lose weight sustainably. Megan lost 80 pounds herself. Here you get healthy, lower calorie recipes!

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