Perfect Butternut Squash Muffins

Looking for a fun way to use up some butternut squash puree? These Perfect Butternut Squash Muffins are a great use for butternut squash puree and are delicious for breakfast, snack, or with some chili!

Four butternut squash muffins on a crumpled up piece of parchment paper with walnuts scattered and the pan of muffins in the background.

Pumpkin always gets the limelight this time of year when it comes to baked goods (who doesn't love Pumpkin Coffee Cake?!), but what about butternut squash? Did you know that you can cook butternut squash, puree it, and use the puree in baked goods, too? You can! It's healthy and delicious.

These butternut squash muffins ended up being a huge hit with my family. Let's talk about them!

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Ingredients in Butternut Squash Muffins

Butternut Squash Muffin ingredients in bowls on a white background - butternut squash, coconut oil, milk, white whole wheat flour, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, eggs, brown sugar, white sugar.
  • Butternut Squash - this recipe is a really fun and unique way to use butternut squash puree. The said, you could use pumpkin puree instead.
  • Eggs
  • Vegetable Oil or Coconut Oil - I have used both of these these in these muffins with great results.
  • Milk - any kind will do. I have made these muffins using cows milk and unsweetened almond milk with good results.
  • Granulated Sugar
  • Brown Sugar
  • White Whole Wheat Flour - this adds whole grains while keeping the muffins light and fluffy.
  • Spices - Cinnamon, nutmeg, and cloves add warm flavors that make these muffins super tasty.
  • Pecans - I enjoy the crunch from the pecans in this recipe but they can be omitted if you like. You could also substitute walnuts.

Butternut Squash Muffins Instructions

The first step to making these muffins is to cook the butternut squash. In the recipe card instructions I include a method to microwave the butternut squash, which I love as far as ease and it's fast. You can also make it in the oven, in which you'll cut the butternut squash in half, scoop out the seeds, place the halves face down on a greased baking dish, pour ½ cup of water on the baking dish and bake at 375 for 45 minutes. This method takes longer, but also does the trick!

Puree the cooked butternut squash using a blender, a food processor, or an immersion blender. You could also mash it up with a fork!

A large glass bowl with pureed squash, eggs, sugars, milk, and oil. The bowl with a whisk in it after the ingredients have been mixed.
  1. In a large bowl, combine the butternut squash puree with granulated sugar, brown sugar, eggs, milk, and oil.
  2. Whisk well.
A glass bowl with the wet ingredients whisked together and the spices, baking powder, baking soda, and salt mixed in.

3. Add the spices, baking soda, baking powder, and salt.

4. Whisk well.

A glass bowl with the flour mixed into the wet ingredients.

5. Add the flour.

6. Using a rubber spatula, fold in the flour until just combined.

A muffin pan with the batter scooped into each muffin cup. One photo has the muffins unbaked and the other has the muffins baked.

9. Divide the batter among 18-20 muffin cups. Fill the cups about ¾ the way full.

10. Bake at 400 degrees for 13-16 minutes.

These were a great breakfast for myself and the kids, along with a healthy and fun snack.

Recipe Tips

Storage. Store these butternut squash muffins in an airtight container for 4-5 days. They will last longer in the refrigerator.

Serving suggestions. These muffins are delicious for breakfast with some eggs and bacon. They also go really well with my favorite Beef Chili or Turkey Chili!

Use frozen butternut squash. If you don't have a fresh butternut squash or they're not in season, look for butternut squash in the freezer section. Simply heat it up and mash.

Four butternut squash muffins on a crumple up piece of parchment paper with walnuts scattered.  One muffin is cut in half and slathered in butter.

Recipe FAQs

Is butternut squash healthy?

Butternut squash is full of good things for us including potassium, fiber, Vitamin A, Vitamin C, and manganese, which can help maintain health bone structure. It's full of antioxidants and is low in calories. It's a great addition to baked goods, like in this healthy muffin recipe!

How should I eat these muffins?

We loved eating these butternut squash muffins slathered in butter, but they would also be great topped with nut butter, apple butter, or just plain!

Can I freeze these muffins?

Yes! Place them in an airtight container and freeze for up to 3 months.

Other Muffin Recipes to Consider

If you make this recipe, please let me know! Leave a ⭐️⭐️⭐️⭐️⭐️ rating on this recipe below and leave a comment, or take a photo and tag me on Instagram with #greensnchocolate.

Butternut Squash Muffins

Perfect Butternut Squash Muffins

Perfect Butternut Squash Muffins are tender, full of warm fall spices, and a creative use for butternut squash!
Print Pin Rate
Course: Breakfast, Snack
Cuisine: American
Prep Time: 20 minutes
Cook Time: 30 minutes
Total Time: 50 minutes
Servings: 18 muffins
Calories: 154kcal


  • 1 ½ cups pureed butternut squash
  • 3 large eggs
  • ½ cup vegetable oil (or melted coconut oil)
  • ½ cup milk
  • ½ cup granulated sugar
  • ½ cup brown sugar
  • 3 cups white whole wheat flour
  • 1 ½ teaspoon baking powder
  • 1 teaspoon baking soda
  • 2 teaspoon cinnamon
  • ½ teaspoon salt
  • ¼ teaspoon ground nutmeg
  • ¼ tsp ground cloves
  • ½ cup chopped pecans (optional)


To make the butternut squash puree

  • Preheat the oven to 400 degrees F.
  • Poke holes in the butternut squash with a fork.
  • Place the butternut squash in the microwave and cook until it is tender, about 10-15 minutes, checking every 3 minutes. Let cool for about 15 minutes.
  • Once cooled enough to touch, cut the butternut squash in half, scoop out the seeds and discard, and then scoop out the flesh, placing it in a bowl. Mash it with a fork.
  • Measure 1 ½ cups of the butternut squash puree.
  • Grease 18 muffin cups
  • In a large bowl, add the 1 ½ cups butternut squash puree, eggs, oil, milk, granulated sugar, and brown sugar, and mix well.
  • Add the baking powder, baking soda, cinnamon, salt, nutmeg, and cloves and fold into the batter until just combined.
  • Fold in the flour.
  • Fold in the pecans, if using.
  • Spoon the batter into the prepared muffin pans, about ⅔ full.
  • Bake in the preheated oven 13-16 minutes, until a toothpick comes out clean.
  • Cool in the pans for about 5 minutes and then remove the muffins and cool completely on a wire cooling rack.
  • Serve topped with butter, nut butter, or plain! Enjoy!


  • You can also use frozen butternut squash in this recipe (which I've done many times!) Simply thaw the squash and then puree in a blender or food processor. 
  • These muffins are great for breakfast or snack, and also delicious served with chili!


Calories: 154kcal | Carbohydrates: 28g | Protein: 4g | Fat: 4g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.003g | Cholesterol: 32mg | Sodium: 142mg | Potassium: 140mg | Fiber: 3g | Sugar: 12g | Vitamin A: 1299IU | Vitamin C: 2mg | Calcium: 56mg | Iron: 1mg
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Recipe Rating


  1. 5 stars
    These muffins were easy to make and were the perfect partner to a bowl of chili. They were also delicious with a swear of butter and drizzle of honey.

  2. 3 stars
    Doubled the recipe to make 24 muffins and could only fit 4 cups flour into the batter. Not sure what happened?

  3. Hello, I have a question before making this recipe.
    Could you be more precise about the weight of the butternut I should use in this recipe please ?
    Where I live we have butternut squashes of all sizes, I'm worried about having too much or too little butternut in the recipe.


  4. I did 1/3 whole wheat, 1/3 all purpose flour and 1/3 unflavored protein powder and it worked great! They weren't too dry, like most muffins w/ protein powder and a handful of chocolate chips was delish!

  5. These are great! Awesome texture and color, very filling, not too sweet. I made them with another type of winter squash, a little less sweet. I used the immersion blender to purée the squash with the oil, brown sugar and maple syrup, and hand-mixed in the beaten eggs afterwards with a fork. I switched most of the sugars for maple syrup (¾ cup of maple syrup replaces one cup of sugar, and the milk has to be cut a bit to balance for the extra liquid). I also replaced the nuts for squash seeds. I put some coconut small pieces on top of some of the muffins and really liked it.