These butternut squash muffins are a healthy, low sugar recipe that’s great for babies, toddlers, adults, and anyone looking for a nourishing snack! They’re made with oats, olive oil, Greek yogurt, squash puree, and plenty of pumpkin pie spice (or cinnamon). You can use leftover cooked squash you have on hand or a can of butternut squash puree. Whip up a batch for weekly meal prep, breakfast, or even the holidays!
Being that this is a Veg World (after all), you probably could have guessed that I’m a big fan of putting vegetables in just about anything. That includes muffins and other baked goods.
Take my Zucchini Carrot Oat Muffins for example. They’re one of the most loved recipes on the site, so I can’t be the only one who likes veggies in her muffins! Of course, I can’t forget about the Veggie Brownies and Apple Beet Muffins. Two of my favs!
And now I’m adding these butternut squash muffins to the mix. They’re such a fun snack that’s wholesome and easy to boot. The recipe is quite low in added sugar, using just a little bit of maple syrup to bring out the natural sweetness of butternut squash, but the flavor is still amazing. Plus, they’re freezer-friendly, toddler-approved, and full of that spiced squash taste that makes such delicious baked goods.
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Ingredients and Substitutions
- Butternut squash puree: You can find cans of this at many grocery stores (and online here), typically right next to canned pumpkin and/or sweet potato (both of which would be a fine substitute, by the way). If you can’t find it, you can also make some really easily at home by pureeing roasted or steamed squash. For more tips, see my tutorial on How to Make Butternut Squash Puree. If you have leftover roasted squash, this recipe is ideal for using it up!
- Greek yogurt: Use plain Greek yogurt of any fat content (I like to use full-fat for reference). If you don’t have this on hand, sub regular yogurt or sour cream.
- Maple syrup: This helps bring out the natural sweetness of the squash, but you can choose to omit it and substitute more unsweetened applesauce or even mashed very ripe bananas if you are making butternut squash muffins for young babies.
- Unsweetened applesauce: A great way to add some sweetness without using refined sweeteners. If you don’t have it on hand, you can replace it with more maple syrup or mashed very ripe bananas.
- Extra virgin olive oil: Canola, avocado, or another vegetable oil would also work. Melted butter or coconut oil are other options.
- All purpose flour: If you need the muffins to be gluten free, sub gluten free 1 to 1 all purpose flour.
- Old fashioned oats: These are also known as rolled oats.
- Pumpkin pie spice: Just sub cinnamon and a pinch of nutmeg if you don’t have this on hand. They’re really good with it though!!
- Vanilla, baking powder, salt
- Additions: Feel free to add ¼ to ½ cup of chopped nuts (i.e. pecans or walnuts) or chocolate chips to the batter. If you want them a little sweeter, sprinkle some brown sugar on top before baking.
Instructions
The full recipe card for healthy butternut squash muffins is at the bottom of the post. Here’s a preview of the steps.
Whisk together the wet ingredients.
In a separate bowl or measuring cup, mix together the dry ingredients. Then, add them to the bowl with the wet ones. Mix until just combined.
Spoon the batter into a muffin tray, filling each cavity about ¾ of the way. I highly recommend using a silicone muffin pan. If you don’t have one, use liners and grease or spray them with nonstick spray to prevent sticking.
Bake at 400 degrees F until a toothpick inserted in the center comes out clean and the tops are very lightly browned, about 19 to 23 minutes.
Storage and Reheating
Store butternut squash muffins at room temp in an airtight container for 2 to 3 days. Put the container in the fridge to extend the shelf life by a few more days. To freeze for later, transfer them to a freezer-safe container or Stasher bag after cooling and freeze for up to 3 months.
You may prefer to wrap each one individually in plastic wrap or parchment or wax paper to prevent freezer burn before freezing. Thaw overnight in the fridge or reheat in the microwave (with the plastic wrap or parchment removed if you used it) in 20-second increments until warmed through.
Serving
These muffins taste delicious cold or warm. I like to heat them up and add butter or peanut butter. Spreading them with a nut butter or even a little Greek yogurt will boost the protein content and make a balanced snack for toddlers.
Adults can even drizzle them with maple syrup or honey for a little extra sweetness. Enjoy the muffins on their own as a snack or as part of a breakfast spread. They would also be a great addition to Thanksgiving dinner.
More Vegetable Muffin Recipes
If you love butternut squash muffins, you may also enjoy:
I’d love to hear how you like this recipe! Rate/review using the stars on the recipe card or in the comments, and follow the Veg World on YouTube, Instagram, Facebook, and Pinterest. Looking for something totally different? Browse the recipe library.
📖 Recipe
Butternut Squash Muffins
Equipment
- Muffin tray (recommend silicone if you have it)
Ingredients
- 1 cup butternut squash puree - canned or cooked and mashed
- 2 eggs
- ¼ cup maple syrup
- ¼ cup unsweetened applesauce
- ½ cup plain Greek yogurt
- ⅓ cup extra virgin olive oil
- 1 teaspoon vanilla extract
- 1 cup all purpose flour - can sub gluten free all purpose
- 1 cup old fashioned oats - get gluten free if needed
- 2 teaspoons baking powder
- ½ teaspoon salt
- 1 tablespoon pumpkin pie spice - can sub cinnamon
Instructions
- Preheat the oven to 400 degrees F/204 degrees C. Use a silicone muffin tray or silicone liners if you have them. If not, grease or spray paper liners and place them in a regular muffin tray.
- In a large bowl, whisk together the butternut squash, eggs, maple syrup, yogurt, oil, and vanilla. In a small bowl, combine the flour, whole oats, baking powder, salt, and pumpkin pie spice. Add the dry ingredients to the wet ones and whisk or stir together. The batter should be lumpy from the oats.
- Use an ice cream scoop or spoon to fill each muffin cavity about ¾ of the way.
- Transfer to the muffins to the preheated oven and bake on the center rack for 19 to 23 minutes, or until a toothpick inserted into the center of a muffin comes out clean and the tops are very lightly browned.
- Remove the muffins from the oven. Let them cool for a few minutes in the muffin tray, then transfer to wire racks to finish cooling. Enjoy!
- Leave a rating or review by tapping the stars on this recipe card (above) or in the comments section (at the end of the post)!
Notes
- Butternut squash puree: Canned butternut squash can be found at most grocery stores, but you can use squash that you cook and mash yourself or sub canned pumpkin. Follow my instructions in my post on How to Make Butternut Squash Puree for more info.
- Sweeteners: To make these muffins without any refined sweeteners (i.e. for young babies under 1), omit the maple syrup and replace with more unsweetened applesauce of mashed bananas. If you want sweeter muffins (i.e. if you’re not making them for kids), replace the applesauce with more maple syrup.
- Additions: Add ¼ to ½ cup of chopped nuts or chocolate chips to the batter before baking. You can also top the muffins with brown sugar or some extra whole oats before putting them in the oven.
- Serving: Enjoy the muffins warm or cold, plain or topped with butter, cream cheese, or nut butter.
- Storage: Store at room temp in an airtight container for 2 to 3 days or in the fridge for up to 5 to 7 days. To freeze, let them cool completely then transfer to an freezer-safe container. If you want to prevent freezer burn, you may prefer wrapping each one in plastic wrap or parchment paper before placing into a container. Freeze for up to 3 months. Thaw in the fridge overnight or in the microwave (with any wrapping removed if you used it) in 20-second increments until warmed through.
Nutrition
This post was originally published in November 2019. It was updated with new photos and slight modifications to the ingredients (replacing half of the original amount of maple syrup with applesauce) in February 2024.
Emily Long
My son and I made these vegan (flax egg, almond milk yogurt) and subbed the applesauce for one very ripe banana. He’s currently gobbling up the batter while our first batch bakes. So far, he seems to love it!
I also roasted some fresh butternut squash before blending it. I’m hoping that adds a little more flavor.
Lizzie Streit, MS, RDN
Hi Emily, I’m thrilled to hear they were a hit! Thanks a lot for leaving a comment with the substitutions you made, as I know that will help other readers too! Great idea to use freshly roasted squash.
Donna Williams
I made this recipe this morning, doubling the ingredients because I always use jumbo muffin tins. Both my husband & I loved them. I used frozen butternut squash that was left over from our garden last year. I also used my canned homemade unsweetened applesauce from last fall that already had cinnamon in it so I didn’t have to use any in the recipe. If I run out of squash I’ll definitely use this recipe using pumpkin instead.
Thanks for a great recipe. 🙂
Lizzie Streit, MS, RDN
Hi Donna, I’m so glad you enjoyed this recipe! I bet it tasted delicious with your homegrown ingredients!
Patricia Evans
Made this with leftover roasted squash. Didn’t have some of the ingredients on hand so I substituted sour cream for the yogurt, steel cut oats for the old fashioned and used cinnamon and nutmeg instead of pumpkin pie spice. Turned out wonderfully! Will definitely make again. Thanks for the recipe.
Lizzie Streit, MS, RDN
Hi Patricia, yay! I’m so glad the recipe turned out well with the modifications you made! Thanks for leaving a review.
Daniella
Made this into a loaf with gf flour. Moist and delicious, thank you for the recipe!
Lizzie Streit, MS, RDN
Yum! Thanks so much for sharing the modifications you made. Glad you enjoyed the recipe!
Michele Bhardwaj
Amazing! Will be using this recipe as a base for other puréed fruit and veg muffins! Love them
Lizzie Streit, MS, RDN
That’s great, Michele! So glad to hear it. Thank you for your 5-star review!