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Butternut Squash Muffins

Oct 13, 2012 | Recipes | 5 comments

These Butternut Squash Muffins are a delicious paleo muffin recipe. The best part? Only 7 ingredients…and one of them is optional!

Leaves changing, temperatures cooling and the return of pumpkin-flavored treats! I love fall and the transition to heartier, warmly spiced foods.

I frequently use butternut squash in my baked goods. It works well as a sub in pumpkin recipes. I buy a larger (3-4 pound) squash and roast whole (about 1-1.25 hours at 350F). Then I have plenty of squash to use in savory and sweet dishes (think creamy pear-squash soup or butternut squash pancakes with pecans & chocolate chips!).  Below is an easy, gluten-free fall treat:

Butternut Squash Muffins
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4.75 from 4 votes

Butternut Squash Muffins (Gluten Free)

Servings: 12
Calories: 180.5kcal


  • 2 cups almond flour
  • 1 tsp baking soda
  • 1 Tbsp pumpkin pie spice
  • 1.5 cups butternut squash, cooked and mashed
  • 1/4 cup maple syrup (OR 4 dates, Medjool preferred)
  • 1 egg
  • 1/2 cup chocolate chips (optional)


  • Stir together dry ingredients (almond flour, baking soda, pumpkin pie spice).
  • In a blender, puree wet ingredients until smooth (butternut squash, maple syrup or dates, egg).
  • Mix wet into dry.
  • Stir in chocolate chips, if using.
  • Pour into muffin papers and at bake at 350F for 20-25 minutes or until tops spring back when pressed. I’ve also made bars by using an 8×8” or 9×9” pan (bake for 35-45 minutes).


*If you don't have cooked butternut squash on hand, you can roast or steam and then mash.
**Nutrition info is for 1 serving and includes maple syrup version and optional chocolate chips.


Calories: 180.5kcal | Carbohydrates: 16.4g | Protein: 5g | Fat: 12.2g

Are these butternut squash muffins healthy?

I can assure you, these butternut squash muffins are just as healthy as they are tasty! Here are some of the nutritional benefits the recipe brings:

Butternut Squash (Vitamin A, Vitamin C, Vitamin E, B Vitamins, Magnesium, Potassium, Folate)

Butternut squash has an extraordinary amount of vitamin A, which makes it excellent for your eyes, bones and immune system. It's also high in antioxidants which can help decrease inflammation and risk for disease. The type of antioxidants found in butternut squash and other yellow and orange fruits and veggies are particularly promising for preventing heart disease.

Almond Flour (Magnesium, Vitamin E, Potassium)

With almonds as the only ingredient, almond flour is a nutritious choice for baked goods. High in magnesium, vitamin E and potassium, almonds are good for your heart and also help lower LDL cholesterol. One serving of almonds also has as much calcium as 1/4 cup of milk!

Cinnamon (Antioxidants)

Frequently used in traditional medicine, cinnamon is good for your heart and also may help stabilize blood sugar. Research also suggests that cinnamon may help lower cholesterol.

Pure Maple Syrup (Manganese, Zinc, Iron, Potassium, Calcium)

1/3 cup of pure maple syrup contains 165% of the recommended dietary intake for manganese and 28% for zinc. It also has a lower glycemic index than table sugar, reducing blood sugar spikes.

Eggs (Vitamin A, B Vitamins, Selenium)

An egg contains 7 grams of protein and is full of lutein (good for your eyes) and choline (good for your brain).

When choosing your eggs, keep in mind that omega-3 eggs offer up to 5 times as much omega-3 in contrast to conventional eggs. In addition, they have almost 40% less of the inflammatory omega-6 fatty acid arachidonic acid. As a result, I think Omega-3 eggs are worth it if you can swing it in your grocery budget.

Similarly, pastured eggs offer far superior nutritional content to conventional eggs. Higher in vitamin A, vitamin D, vitamin E, and omega-3, they're certainly a better choice than conventional if available to you.

Have you tried using butternut squash in baked goods? Share your ideas and pictures on Facebook, Twitter or Instagram as @prepdish in all 3 places, or leave a comment below.

More Paleo Muffin Recipes

Looking for more paleo muffin recipes? I've got you covered!

Even if you're not paleo, these muffins are far more satisfying than traditional muffins that are all carbs. They each contain a healthy balance of protein, healthy fats and carbs for a snack or breakfast that actually fills you up!

Gluten Free Chai Spice Muffins

Chai Spice Muffins

My paleo chai spice muffins use a mix of almond flour and coconut flour. If you haven't tried coconut flour, I highly recommend it. It's an inexpensive ingredient and really gives gluten free and paleo baked goods a great texture.

The cinnamon, cardamom, ginger and cloves give these such a deliciously spiced flavor!

Paleo Berry Muffins

Very Berry Muffins

The addition of raspberries really sets these apart from your standard blueberry muffin. Flax is a key ingredient in this paleo muffin recipe, providing plenty of omega-3s and B vitamins. These also contain 5 eggs, and so quite a bit of protein.

Gluten Free Banana Muffins

Paleo Banana Nut Muffin Recipe

It doesn't get much more classic than banana nut muffins and for good reason! These have all the classic flavor of the muffins you enjoyed as a child but, with ingredients like almond butter, coconut oil and coconut flour, are much more nutritious.

Tips on How to Use Butternut Squash

How to Use Butternut Squash

Butternut Squash is one of the tastiest fall ingredients out there but it can be a bit intimidating if you haven't used it before.

Learning the easiest and safest way to chop various fruits and veggies allows you to confidently incorporate so much more variety into your family meals. I love sharing the tips and knife skills I learned in culinary school for this very reason. If you find chopping butternut squash tedious or difficult, watch my short video here to see how! (I share other culinary how-to videos on my YouTube channel here!)

You can also see my favorite way to cook the “bulb” of the butternut squash here. This part of the gourd can be tricky to chop, so I avoid chopping it altogether! It's delicious whole-roasted.

If you have extra butternut squash after making your muffins, here are a few other delicious ways to use it:

FAQ – Common Questions for Butternut Squash Muffins

Do you have to peel butternut squash before baking?

No, you do not have to peel butternut squash before baking. You can simply cut in half, scoop out the seeds, and roast it. After roasting, you can either eat the squash with the peel or easy scoop it out with a spoon. I sometimes peel and chop the top of the squash, and simply cut the bottom half in two and scoop out the seeds.

Should butternut squash be cooked face up or face down?

Rub your squash with a bit of oil and cook roast with the cut side face down on the pan.

Can you freeze butternut squash muffins?

Yes! I'm a big fan of freezing muffins, including butternut squash muffins, for an easy, grab-and-go breakfast or snack. I recommend flash freezing – place cooled muffins on a baking sheet in freezer. Once frozen, transfer to a freezer container.

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Gluten Free Butternut Squash Muffins
Beginner Menu Guide


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  1. Amnah

    Can I substitute oats for almond flour?

    • Meri Raffetto

      It’s always tricky substituting flour with baked goods but you can try!

  2. Santei Di Leonardo

    Hi, how do you recommend cooking the chopped butternut squash? just boil & drain it? If so, how long does it take to boil?

    • Meri Raffetto

      You can roast it or steam it until it’s fork tender and then mash!

  3. Sheri

    I made these and they are delicious!! I added a pinch of salt and some chopped toasted pecans. The mini chocolate chips are perfect in this recipe! I gave some to a friend and she wants the recipe. Thank you


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