Butternut Squash Muffins Recipe

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These butternut squash muffins are a perfect way to enjoy the more subtle flavors of fall!

This time of year, good things come in the form of squash. So next time you pick up a butternut squash at the grocery store, keep these muffins in mind as a great way to use some of it up!

Two Butternut Squash Muffins in a row on a white, marble surface.

Gluten-Free Recipe

Normally when I bake, I would use a whole wheat flour of some sort, instead of all purpose flour, like most people use. But for this muffin recipe, I wanted something gluten-free as well. So I used a gluten-free flour and I was not disappointed. The top of the muffins will not rise into domes the way many muffins do. But I find that makes it easier to spread butter on them anyway.

Butternut Squash

Where many recipes like this would involve butternut squash puree, this recipe uses small chunks of whole butternut squash. I find that the muffins bake much better this way.

You can use just about any winter squash in this recipe. It doesn’t have to be butternut. You could easily make these into pumpkin muffins by using pumpkin. This is a great recipe for using up any leftover squash from another meal. I can highly recommend acorn squash or Kabocha squash as well. Get creative!

The Spices

If you don’t have all the spices listed below, you can replace them with 1 tbsp. pumpkin pie spice.

A stack of muffins on a cutting board with a whole butternut squash laying behind them.

How To Serve Butternut Squash Muffins

  • apple butter
  • butter + maple syrup
  • jam

Ingredient Checklist

2 cups oat flour – If you being gluten-free is critical for you, make sure you purchase oat flour that is labeled as such. Oats can be highly cross-contaminated.

¼ cup arrowroot powder – In a pinch, you can substitute this with cornstarch.

1 tbsp. baking powder – Make sure it’s newer. Older baking powder won’t do the same job.

2 tsp. ground cinnamon

1 tsp. ground nutmeg

¼ tsp. ground allspice

¼ tsp. ground cloves

½ cup granular sweetener – Any unprocessed sweetener that is similar to brown sugar. Sucanat, coconut sugar, and monk fruit are all good options.

1 cup diced butternut squash – diced at ¼ inch. You want these small so they bake fully. Note that you can use sweet potato in place of the squash if you prefer that.

2 large eggs – These can be cold or room temperature. But room temperature works best.

1 cup unsweetened almond milk – You can use regular milk instead if dairy isn’t a problem for you.

¼ cup oil – I used coconut oil, but any healthy vegetable oil will work. Even a light flavored olive oil will work fine here.

½ cup unsweetened apple sauce – Make sure it’s unsweetened, or your muffins will be too sweet.

Extra Additions

  • Dark chocolate chips – ½ to 1 cup
  • Chopped walnuts – ½ to 1 cup
  • Pure vanilla extract – 1-2 tsp.
  • Fresh ginger – 1 tsp. grated
Four Butternut Squash Muffins together with a fifth sitting on top of them.

How To Make Butternut Squash Muffins

A muffin pan with foil liners in it.

Preheat oven to 350 degrees F. and line your muffin tin with foil or paper liners. Foil liners work best. If you are using a silicone muffin pan, you don’t need to use the liners.

All the dry ingredients for this Butternut Squash Muffins Recipe mixed together in a mixing bowl.

In a large bowl, whisk flours, spices, baking powder, and sweetener (all the dry ingredients) together.

The cut butternut squash pieces being stirred into the dry mix.

Stir in the butternut chunks to coat them well with the flour mixture.

The wet ingredients added to the dry ingredients.

Make a well in the middle and add the wet ingredients. Stir well.

The raw batter sitting in the muffin pan.

Spoon the muffin batter into the muffin cups, using a rubber spatula to get all the batter.

Butternut Squash Muffins cooling on a black, wire, cooling rack.

Place in preheated oven and bake for 40 minutes or until a knife poked in the middle of a muffin comes out clean. Cool to room temperature on a wire rack.

How To Store Butternut Squash Muffins

Store these muffins in an airtight container and store them in the fridge for up to 4 days.

Freezing Muffins

You can easily freeze these! Wrap them well and keep them in an airtight container in the freezer for up to 4 months. Set in the fridge overnight to thaw or heat in a microwave.

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More Healthy Muffins

Butternut Squash Muffins Recipe

Two Butternut Squash Muffins in a row on a white, marble surface.

Butternut Squash Muffins

Delicious muffins made with butternut squash!
Print Pin Rate
Course: Breakfast, Snack
Cuisine: American
Servings: 16 muffins
Calories: 144kcal
Author: The Gracious Pantry

CLICK TO WATCH THIS RECIPE IN ACTION!

Ingredients

  • 2 cups oat flour
  • ¼ cup arrowroot powder
  • 1 tbsp. baking powder
  • 2 tsp. ground cinnamon
  • 1 tsp. ground nutmeg
  • ¼ tsp. ground allspice
  • ¼ tsp. ground cloves
  • ½ cup granular sweetener
  • 1 cup diced butternut squash (diced at ¼ inch)
  • 2 large eggs
  • 1 cups unsweetened almond milk
  • ¼ cup oil
  • ½ cup unsweetened apple sauce

Instructions

  • Preheat oven to 350° F. and line your muffin tin with cupcake papers. Foil papers work best.
    A muffin pan with foil liners in it.
  • In a medium mixing bowl, whisk together your flour, spices, baking soda and sweetener.
    All the dry ingredients for this Butternut Squash Muffins Recipe mixed together in a mixing bowl.
  • Stir in the butternut and apples to coat them well with the flour mixture.
    The cut butternut squash pieces being stirred into the dry mix.
  • Make a well in the middle and add the rest of the ingredients. Stir well. This should be a thick batter, but you should also be able to stir it.
    The wet ingredients added to the dry ingredients.
  • Fill your muffin papers.
    The raw batter sitting in the muffin pan.
  • Bake for 40 minutes or until a knife poked in the middle of a muffin comes out clean. Cool on a wire rack.
    Butternut Squash Muffins cooling on a black, wire, cooling rack.

Notes

Please note that the nutrition data given here is a ballpark figure. Exact data is not possible.

Nutrition

Serving: 1muffin | Calories: 144kcal | Carbohydrates: 21g | Protein: 3g | Fat: 6g | Saturated Fat: 1g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 3g | Trans Fat: 1g | Cholesterol: 23mg | Sodium: 34mg | Potassium: 181mg | Fiber: 2g | Sugar: 7g | Vitamin A: 967IU | Vitamin C: 2mg | Calcium: 72mg | Iron: 1mg

Recipe from the Gracious Pantry® archives, originally posted 1/16/2016.

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2 Comments

  1. Would you be able to use coconut flour or almond meal instead?

    1. The Gracious Pantry says:

      Karen – You could possibly try a combo of both. They are often used together. But I haven’t tried it, so I’m not sure how it would turn out. I may do a paleo version in the near future though.

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