Simple Gluten Free Butternut Squash Muffins

by From Scratch Farmstead
simple gluten free butternut squash muffins

There are cheers all around when these gluten free butternut squash muffins show up for breakfast or a quick snack. You can whip them up in just a few minutes and they freeze very well. And, as far a gluten free baking recipes go, the texture is excellent and they only require a few staple ingredients.

Similar to our gluten free apple bread, these gluten free butternut squash muffins are a staple around here, especially in these fall months.

cultured cream frosting on butternut squash muffins

Why Butternut Squash

It’s no secret that butternut squash are one of our favorite crops to grow and eat. For the last couple of years, we harvested well over one hundred butternut squash and other winter squash. The great thing about butternut squash is that they store extremely well for months. When allowed to properly cure and be kept in a cool environment, we’ve successfully stored butternut squash for as long as a whole year.

roasted butternut squash for puree

Butternut squash are also extremely versatile. From peeling and cubing as a side. To pureeing to use in baking or as a side. To blending into soups, stews, or ground meat dishes such as meat loaf or meatballs. Or, even adding them to a casserole like our butternut squash lasagna or butternut squash enchilada casserole as a replacement for noodles or tortillas respectively. We share all about the many uses of butternut squash in our post, How To Roast Butternut Squash.

Nutrition of Butternut Squash

The deep orange color of butternut squash is indicative of excellent nutrition and being an excellent source of vitamins and minerals. It is a great source of vitamin A, vitamin C, thiamin, niacin, vitamin B6, folate, pantothenic acid, calcium, iron, phosphorus, potassium, magnesium, and manganese.

Can you Substitute Butternut Squash for Pumpkin?

Yes! In fact, I recently learned that canned pumpkin from the store is actually often made with winter squashes like butternut squash instead of actual pumpkin.

how to roast butternut squash and make puree

While butternut squash makes a perfect one-to-one substitute with the puree of a pie pumpkin, we actually strongly prefer butternut squash to pumpkin.

The creamy texture of butternut squash is ideal for baking and pies. We also find it to be thicker and less watery than pie pumpkins. And, there is no comparison when it comes to the vibrant orange of butternut squash.

Gluten Free Butternut Squash Muffins – The Ingredients

Gluten free baking can be tricky. My goal when baking with gluten free ingredients is always to make the recipes as simple as possible with minimal ingredients. But, to still have an excellent taste and texture. 

After a lot of experimentation with different flours and ratios, my go-to starting place for a lot of baked goods is to use a one-to-one ratio of coconut flour and arrowroot or tapioca flour (they can be used interchangeably with one another). I’ve found this combo to generally work very well and now these two ingredients are a staple in our pantry.

gluten free butternut squash muffins ingredients

The ingredients:

Eggs

This is the one common allergen that these muffins do contain and I’ve never tried making it with an egg substitute. But I love that there are 4 eggs in these gluten free butternut squash muffins to give it a boost of protein meaning it’s more satisfying and will keep you fuller longer than a lot of sweet muffins.

Coconut Oil

I normally use melted coconut oil as the fat in this recipe but have substituted leaf lard or melted butter with great results if dairy is an option for you.

Maple Syrup or Honey

Maple syrup is my favorite sweetener to use in this recipe because it pairs perfectly with the butternut squash puree. But honey is a great choice as well. In a pinch I have substituted brown sugar or even cane sugar and they worked ok too.

Butternut Squash Puree

What would a butternut squash muffin be without butternut squash puree. Roasting and pureeing your own butternut squash at home is super easy, and the texture, flavor, and color cannot be beat! You could use pureed pumpkin or any other sort of winter squash as a replacement if needed.

butternut squash puree for muffins

Coconut flour

As I mentioned above, this recipe contains a 1:1 ration of coconut flour and tapioca starch. Coconut flour is known for being incredibly absorbent, hence why there are 4 eggs needed for this recipe.

Tapioca Starch

Tapioca starch or arrowroot powder can be used interchangeably in most recipes. It is also very absorbent and is my go-to thickener for soups and sauces like our homemade enchilada sauce.

Baking Soda

We usually have Bob’s Red Mill Baking Soda on hand at all times to give our baked goods the perfect rise.

Cinnamon

You can feel free to go crazy here with the fall spices like nutmeg, ginger, or cardamom. But we have found that a heaping teaspoon of cinnamon in these gluten free pumpkin muffins does the trick!

Gluten Free Butternut Squash Muffins – 3 Ways

The base gluten free butternut squash muffin recipe is the same, but there are several variations that are possible to fit any occasion.

1. Gluten Free Butternut Squash Muffins with Cinnamon Sugar – After batter has been spooned into muffin cups, sprinkle a mixture of cinnamon and brown sugar (or white sugar) over your muffins before baking.

gluten free butternut squash muffins

2. Chocolate Chip Gluten Free Butternut Squash Muffins – After you finish whisking in your dry ingredients with your wet ingredients, add ½ cup (or more) of chocolate chips to your batter. For an extra treat, throw a few chocolate chips on top of your muffins after spooning them into your muffin cups.

3. Gluten Free Butternut Squash Muffins with Cultured Cream Frosting – When muffins have finished baking, mix a few tablespoons of cultured cream (or cream cheese) with a bit of honey, maple syrup, or dulce de leche. Spoon over cooled muffins for a treat more reminiscent of a cupcake.

homemade cultured cream frosting on butternut squash muffins

Gluten Free Butternut Squash Muffins Recipe

Ingredients:

4 eggs
1/3 cup coconut oil, melted
1/3 cup maple syrup or honey
½ tsp apple cider vinegar
1 cup butternut squash puree
½ cup coconut flour
½ cup tapioca flour (or arrowroot starch)
½ tsp baking soda
1 heaping teaspoon of cinnamon

gf butternut squash muffins with cinnamon sugar topping

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Directions:

1. Mix wet ingredients (eggs, melted coconut oil, maple syrup or honey, apple cider vinegar, and butternut squash puree) together.

2. Add dry ingredients (coconut flour, arrowroot starch, baking soda, and cinnamon).

3. Whisk well to combine. 

4. If adding chocolate chips mix in now, otherwise, spoon into muffin cups.

5. Sprinkle on cinnamon sugar if desired.

6. Bake at 350 degrees for 18-20 minutes.


For another gluten free muffin, our gluten free chocolate beet muffins are another family favorite.

gluten free butternut squash muffins

Gluten Free Butternut Squash Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes

There are cheers all around when these gluten free butternut squash muffins show up for breakfast or a quick snack. You can whip them up in just a few minutes and they freeze very well. And, as far a gluten free baking recipes go, the texture is excellent and they only require a few staple ingredients.

Ingredients

  • 4 eggs
  • 1/3 cup coconut oil, melted
  • 1/3 cup maple syrup or honey
  • ½ tsp apple cider vinegar
  • 1 cup butternut squash puree
  • ½ cup coconut flour
  • ½ cup tapioca flour (or arrowroot starch)
  • ½ tsp baking soda
  • 1 heaping teaspoon of cinnamon

Instructions

    1. Mix wet ingredients (eggs, melted coconut oil, maple syrup or honey, apple cider vinegar, and butternut squash puree) together.
    2. Add dry ingredients (coconut flour, arrowroot starch, baking soda, and cinnamon).
    3. Whisk well to combine.
    4. If adding chocolate chips mix in now, otherwise, spoon into muffin cups.
    5. Sprinkle on cinnamon sugar if desired.
    6. Bake at 350 degrees for 18-20 minutes.

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