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Spiced Butternut Squash Muffins

Spiced Butternut Squash Muffins

Move over pumpkin! These spiced butternut squash muffins are yummy and healthy enough to eat for breakfast. They are dairy-free and can be easily modified to be vegan. Can't wait to get started? Jump to the recipe!

It seems like pumpkin puree gets all of the attention when it comes to baking, but don’t overlook butternut squash puree. It’s a great substitute for pumpkin in most recipes, and it also stands out as a fabulous baking ingredient in its own right. Not only does it add moisture and wonderful flavor to baked goods, but butternut squash (and other winter squashes) are also chock full of Vitamin A. It also delivers a healthy dose of vitamin C, Vitamin E, and folate. You can check its full nutrition profile here.

We currently have a surplus of winter squash at our house, and I’ve been searching for creative ways to use it all! I’ve also been pureeing and freezing like a madwoman to make sure it doesn’t go to waste (learn to make the puree here!). These Spiced Butternut Squash Muffins are one of our favorite recipes so far. My son and I have made them the last three weeks in a row. And yes, I realize that baking them into muffins isn’t exactly the healthiest way to eat them, I’d say these muffins contain more nutrition than your average morning muffin, especially since they’re made with whole wheat flour.

One tip: Don’t accidentally snort nutmeg up your nose! The last time my son and I made these, I was encouraging him to smell the spices to help him learn to identify them all by taste, sight, and scent. Unfortunately, I didn’t realize how full the nutmeg container was. When I went to sniff it, I got a ton of nutmeg up my nose. It was sooooo painful!! It took hours for it to finally clear. It was like getting a ton of chlorine up my nose, but worse, and it lasted way longer. Ugh! The moral of the story? Sniff nutmeg carefully.

However, these muffins are so yummy, the pain was worth it.

Here’s how to make them:


  • 2 cups white whole wheat flour

  • 2 tsp baking powder

  • 1 tsp baking soda

  • ¾ cups brown sugar

  • 1 egg (or 1 flax egg)

  • ⅓ cup coconut oil

  • 1 cup butternut squash puree (fresh, frozen, or canned)

  • 1 tsp cinnamon

  • ¼ tsp nutmeg

  • ½ tsp ginger

  • 1 cup chocolate chips, walnuts, or ½ cup of each (optional)


  1. Preheat the oven to 350 degrees.

  2. If your coconut oil is solid, melt it in the microwave and allow it to cool. Then, mix together the coconut oil, egg, and sugar until fully combined.

  3. Add the butternut squash to the coconut oil/egg/sugar mixture.

  4. In a separate bowl, combine your dry ingredients (flour, baking soda, baking powder, and spices) and gently mix them together with a wooden spoon until all of the ingredients are evenly distributed.

  5. Slowly add the dry ingredients to the wet ingredients, stirring as you go. Be careful not to overmix.

  6. Add the chocolate chips and/or walnuts (if using)

  7. Distribute the batter into 12 standard-sized, parchment-lined muffin cups.

  8. Bake at 350 degrees for 25 minutes, or until a toothpick or fork inserted into the center comes out clean.

  9. Cool before eating and enjoy!

To make your own Butternut Squash puree:

Making your own butternut squash puree is simple:

  • Cut your butternut squash in half.

  • Scoop out the seeds and dark orange, stringy flesh

  • Place your squash halves in a crockpot.

  • Bake on high for approximately 4 hours. There is no need to add extra water.

  • You'll know the squash is done when it can be easily pierced with a fork. Allow them to cool and then scoop out the flesh with a spoon.

  • I find that butternut squash is so soft, there is no need to puree it any further, though you can puree it in a food processor or blender if you wish.

  • Store in an airtight container. Frozen butternut squash will keep in the freezer for about 6 months. It will keep in the refrigerator for up to a week.

If you're looking for more recipes to use up your pumpkin or winter squash, be sure to check out my posts on:

Printable & Pinnable Recipe Card:

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