With a dose of butternut squash and apple butter, these Butternut Squash Muffins pack a lot of flavor, moisture, and nutrition in one easy to eat, delicious package. They’re a healthy muffin to serve at any time of the day.

butternut squash muffins on wire rack

Butternut Squash Muffins

The warm spices of fall pair with butternut squash puree in these easy muffins. They’re just sweet enough to be enticing and have whole grains in the mix.

I love making super healthy muffins for kids that can be breakfast, a snack, or an easy side dish. In fact, muffins are one of the things I make almost every week because I love having them on hand in the fridge. Let’s be real… sometimes us parents need a hand-held meal just as fast as the kids do!

We love them as an easy toddler breakfast or as a side with soup or chili, such as Vegetarian Bean Chili, White Turkey Chili, or Macaroni Soup.

TIP: With both a vegetable and a fruit packed inside, these are an extra-nutritious snack.

ingredients in butternut squash muffins

Ingredients You Need

Here’s what you’ll need to make these healthy muffins so you know what to have on hand and ready to go.

Step-by-Step Instructions

Here’s a look at the easy process involved in making this muffin recipe. Scroll down to the bottom of the post for the full information.

how to make butternut squash muffins step by step
  1. Preheat the oven and grease a muffin tin.
  2. Stir together the dry ingredients and the wet ingredients in two separate bowls.
  3. Spoon the batter evenly into the muffin cups,.
  4. Bake until a cake tester inserted into the center comes out cleanly.

TIP: You can bake these ahead of time and warm for 10 seconds in the microwave and serve whenever you’d like!

butternut squash muffins cooling on rack

Frequently Asked Questions

What kind of butternut squash is best in these muffins?

You can use any mashed butternut squash puree—either a mashed butternut squash, butternut squash baby food puree, or canned butternut squash.

Can I make these ahead of time?

Yes! They store for 3-5 days in the fridge in an airtight container or in the freezer for up to 3 months stored in a zip top bag. Thaw in the fridge or briefly in 15 second increments in the microwave.

What kind of icing do you add?

I sometimes mix together ¼ cup powdered sugar with 1-2 teaspoons milk and drizzle it over the top for an extra bit of fun.

What should I serve these with?

These healthy muffins are good on their own, topped with a little cream cheese, or smeared with nut butter. (You’d also be well-served serving them warm topped with a little butter!)

sliced butternut squash muffins on pink plate

Best Tips for Success

I’d love to hear your feedback on this recipe if you try it out in your home, so please comment below!

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Butternut Squash Muffins

These moist muffins are great on their own or topped with butter, honey, or apple butter. Try them for breakfast, snack, or as a side for dinner.
4.96 from 23 votes
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Cuisine American
Course Muffins
Calories 138kcal
Servings 10


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  • Preheat the oven to 375 degrees F and grease 10 cups of a standard muffin tin.
  • Stir together all ingredients in a medium bowl.
  • Spoon the batter evenly into the muffin cups, using about ¼ cup batter in each one.
  • Bake for 20-22 minutes or until a cake tester inserted into the center comes out cleanly. Let rest in the pan for a few minutes, then remove from the pan and let cool on a wire rack.


  • Store for up to 5 days in an airtight container in the fridge or in a zip top freezer bag in the freezer for up to 3 months.
  • Use leftover mashed butternut squash or canned or baby food squash puree.
  • Top with apple butter, cream cheese, nut or seed butter, or regular butter as desired.
  • You can use pumpkin puree instead of butternut squash if desired.
  • Apple butter and applesauce work the same in this recipe.
  • Dairy-free: Use nondairy milk and neutral oil.
  • Gluten-free: Use a 1:1 style cup for cup gluten-free flour and certified gluten-free oats to make these gluten-free.


Serving: 1muffin, Calories: 138kcal, Carbohydrates: 22g, Protein: 4g, Fat: 4g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 1g, Cholesterol: 40mg, Sodium: 123mg, Potassium: 150mg, Fiber: 2g, Sugar: 6g, Vitamin A: 1250IU, Vitamin C: 2mg, Calcium: 82mg, Iron: 1mg
Tried this recipe?Rate in the comments and tag @yummytoddlerfood on IG!

This post was first published November 2018.

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4.96 from 23 votes (12 ratings without comment)

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  1. 5 stars
    My son loved these!! He devoured them. Can’t wait to try these with different veggies like sweet potatoes or carrots. We substituted coconut milk for the milk and oat flour for the oats, but it worked perfectly!

  2. 5 stars
    I want to make tbis as a cake but NO oats and NO wheat flour. Will that still work with white flour? How much time for a sheet pan cake? 45 min?
    Thanks for your help. We have diabetics and dieters!

    1. Hi- I haven’t made it with all of those changes so I can’t say for sure. I would sub all purpose flour for the flour and oats, and double the recipe to make a 9×11-inch cake. (Or any size larger than 8×8.) I would guess 26-28 minutes, but you’ll need to check the middle with a cake tester.

  3. Excited for my babe to have these but ran into some issues making them just now. Took them out after about 25 minutes and the batter was still gooey on the inside. I ended up having to bake them another 10-15 min or so and now of course the outside is nearly burnt and hard, but the insides are just barely done. Any idea what went wrong? I followed the recipe exactly.

  4. 5 stars
    I ended up being that person and realizing that I didn’t have all of the ingredients halfway through the recipe, ha! However, subbing an overripe banana for my (moldy) applesauce worked out well. Great recipe!

      1. Which recipe was it for? If you have trouble with muffing baking through, try replacing your baking soda. Hope that helps!

  5. 5 stars
    These are very good and light. Easy using frozen butternut squash. I also made them with applesauce I made with carrots and butternut squash, so there’s even more squash in there. (:

  6. 5 stars
    These came out similar to the sweet potato muffins and I’m not sure if me or my son like them more! Came out super fluffy and they smelled amazing while in the oven lol