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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 it and are delicious for breakfast, snack, or with some chili!

Butternut Squash Muffins

Pumpkin always gets the limelight this time of year when it comes to baked goods, 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!

Health Benefits of Butternut Squash

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!

Perfect Butternut Squash Muffins

Ingredients in Butternut Squash Muffins

  • 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
  • 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
  • Spices - Cinnamon, nutmeg, and cloves add warm flavors that make these muffins super tasty.
  • Baking Powder
  • Baking Soda
  • Salt
  • 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

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

Combine the ingredients. After making the butternut squash puree, you combine it with granulated sugar, brown sugar, eggs, milk, and oil. Last you mix the dry ingredients in with the wet ingredients with a rubber spatula. I used white whole wheat flour which I love using in my baked goods. It adds whole grains but still has a light texture. You can certainly use all-purpose if you prefer. The other dry ingredients include cinnamon, nutmeg, cloves, salt, baking soda, and baking powder.

Add the pecans. Fold in chopped pecans to the muffin batter mixture. The pecans are optional, so you do you!

Bake. Divide the batter between the muffin tin (this recipe makes 24 muffins) and then bake at 400 degrees for 14-16 minutes.

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

Perfect Butternut Squash Muffins

Butternut Squash Muffin Tips

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

Freeze. You can freeze these muffins, too! Place them in an airtight container and freeze for up to 3 months.

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.

Like this recipe? Check these out, too!

Maple Donut Muffins

Pumpkin Coffee Cake

Apple Butternut Squash Muffins from Family Food on the Table


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
Cuisine: American
Prep Time: 20 minutes
Cook Time: 30 minutes
Total Time: 50 minutes
Servings: 12
Calories: 332.9kcal


  • 1 small 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 pecan (optional)


  • Preheat the oven to 400 degrees F.
  • Grease 24 muffin cups
  • 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.
  • 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 flour, baking powder, baking soda, cinnamon, salt, nutmeg, and cloves and fold into the batter until just combined.
  • Fold in the pecans, if using.
  • Spoon the batter into the prepared muffin pans, about ⅔ full.
  • Bake in the preheated oven 14-16 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!


Calories: 332.9kcal | Carbohydrates: 47.4g | Protein: 7.17g | Fat: 14.62g | Saturated Fat: 8.34g | Cholesterol: 53.75mg | Sodium: 218.35mg | Potassium: 367.29mg | Fiber: 4.86g | Sugar: 19.35g | Vitamin A: 6736.76IU | Vitamin C: 13.13mg | Calcium: 105.21mg | Iron: 1.64mg
Tried this recipe?Mention @greensnchocolate to let me know!
Need more ideas?Find all of my recipe pins @greenschocolate

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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.