Whole Grain Pumpkin Spice Butternut Squash Muffins

Whole Grain Pumpkin Spice Butternut Squash Muffins

These whole grain pumpkin spice butternut squash muffins are a healthy, flavorful, aromatic, and fluffy treat that are perfect for fall! 

Whole Grain Pumpkin Spice Butternut Squash Muffins

The temperatures are dipping, the colors are changing, and race season has begun again, which you know what that means: autumn is arriving soon!

Fall is my absolute favorite month. One of the reasons why? In addition to the weather, colors, attire, and running, I adore fall harvest foods. I could probably live on them throughout the entire year, particularly winter squashes.

Supposedly, you can store winter squash for a better part of a year in a cool dark pantry, but for some reason mine never make it that long, and it’s not because they spoil.

During the season that is all the range for everything pumpkin, I savor the other winter squashes: butternut, kabocha, and acorn. So, brace yourselves for what will be an inevitable influx of winter squash recipes on the blog!

Whole Grain Pumpkin Spice Butternut Squash Muffins

One of the first recipes I tested and shot for the upcoming Eat to Run e-cookbook was a butternut squash almond bread. Oh my goodness, was it delicious! We devoured the two test loaves in no time flat, and since then, I’ve been restless to bake again with butternut squash.

Butternut squash has a vibrant and sweet flavor to it that rivals that of pumpkin. Supposedly, butternut squash actually makes a better pie than pumpkin, and I’ll let you know whether that accurate or not in a few weeks when I whip up a butternut squash pie for Ryan’s birthday.

Butternut squash not only tastes good; it is abundant in vitamins and minerals. Its vitamin A will boost your immune system, maintain healthy vision, and promote bone metabolism (the continual regrowing of new bone tissue). Its vitamin C plays a key role in recovery by lessening oxidative stress. Niacin (vitamin B3) promotes healthy cholesterol levels and overall cardiovascular health. Iron fights fatigue and boosts your athletic performance. Magnesium promotes better sleep, increases your energy levels, and improves your body composition. Doesn’t that all make you want to dig into a big dish of butternut squash?

Whew, that was a science lesson! As a reward, let’s have some muffins!

Whole Grain Pumpkin Spice Butternut Squash Muffins

These whole grain pumpkin spice butternut squash muffins are a subtly sweet, fluffy, and aromatic treat that are as healthy as they are delicious. When I say fluffy, I mean light, tender, melt-in-your-mouth mountains of goodness.

As the title suggests, these pumpkin spice butternut squash muffins are 100% whole grain! They contain oats and whole wheat flour. I always use Bob’s Red Mill Whole Wheat Flour since it has a fine, stone-ground texture; a whole wheat pastry flour would work well also.

Sometimes whole wheat flour can often produce a dense and less-than-desirable baked good. Not the case with here! Double leaving and an increased baking temperature provide these butternut squash muffins with plenty of volume and a light, airy texture.

Since I’ve been eating less sugar lately, my palate has become more sensitive to sugar, so I concocted a muffin that only offered a subtle touch of sweetness. The lower-sugar content makes these ideal for anyone watching their weight or trying to eat high-quality foods during the peak of training. If you crave a sweeter muffin, please check the notes on the recipe below.

Whole Grain Pumpkin Spice Butternut Squash Muffins

Finally, I used homemade butternut squash puree for these muffins! You can purchase butternut squash puree in some stores, but the process to make it requires very little effort. Plus, homemade squash puree tastes better, is fresher, and is extremely budget-friendly. First, you peel the squash with a sharp knife and chop it up into small pieces (approximately 1-inch in diameter). Then, you steam the squash over medium heat in a pot or pan (with a small layer of water at the bottom) for 10-20 minutes (depending on the size of your squash). Once the squash is tender and can easily be pierced with a fork, remove from heat and let cool for 5-10 minutes. Use your food processor to puree it up. Half of a butternut squash usually makes about 2 cups of puree.

Note: If you do not eat these within three days, freeze to preserve optimal taste and texture.  

Whole Grain Pumpkin Spice Butternut Squash Muffins

Laura Norris
5 from 1 vote
Prep Time 10 mins
Cook Time 14 mins
Total Time 24 mins


  • 1/2 cup rolled oats
  • 1/2 cup milk of choice + 2 tablespoons divided
  • 2 cups whole wheat flour
  • 2 teaspoon baking powder
  • 2 teaspoon baking soda
  • 1/2 teaspoon cinnamon
  • 1 teaspoon pumpkin pie spice
  • 1/4 teaspoon salt
  • 1 1/2 cups butternut squash puree*
  • 1 large egg
  • 4 tablespoons unsalted butter melted**
  • 1/3 cup brown sugar***
  • 2 tablespoons maple syrup


  • Preheat your oven to 400 degrees Fahrenheit.
  • Soak the oats in 1/2 cup milk for 5 minutes to soften.
  • Combine the flour, baking powder, baking soda, cinnamon, pumpkin pie spice, and salt in a large mixing bowl.
  • In a separate mixing bowl, whisk together the butternut squash puree, egg, brown sugar, and maple syrup.
  • Stir the oat and milk mixture into dry ingredients. Form a well in the center and pour in the wet ingredient mixture. Lightly whisk together. Gently fold the butter and remaining milk into the batter.
  • Grease or line the cups of your muffin pans and divide the batter evenly amongst the 12 tins.
  • Bake for 12-14 minutes, until the domes are peaked and an inserted toothpick comes out clean.


*See post for directions on how to make your own butternut squash puree.
**You can substitute coconut butter if desired, but don't use applesauce or yogurt - the final product will be too moist.
***For a sweeter muffin, increase the sugar to 1/2 cup.
Store in an airtight container lined with paper towels for 1-3 days. You can also freeze for optimal taste and texture, especially if you do not plan on eating the whole batch within 3 days.

Whole Grain Pumpkin Spice Butternut Squash Muffins

I’ll be linking up for Meatless Monday with Tina and Deb. Be sure to check out my and other meatless recipes on Monday!

Meatless Monday

Questions of the Day:
Do you like winter squash? Which one is your favorite?
Who else has started eating everything pumpkin?

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37 Responses

  1. I get really excited to see recipes I want to make and that I have all of the ingredients for already in my house! I just bought a big butternut squash yesterday! It’s my favorite :). I may make these muffins this weekend. I had bought the squash for the jewish holidays (was planning to roast it with sweet potatoes and acorn squash) but maybe I will save some for muffins. Thanks!

  2. I’m a bit of a rebel, so I don’t eat pumpkin stuff. I don’t like pumpkin pie but the butternut squash pie intrigues me! I bet I’d like that.

    1. I used to not like pumpkin pie at all – I don’t think I ate it from age 13-22. Pumpkin is good and all, but butternut is so much better, so hopefully the case is so for the pie!

  3. Obsessed with all things acorn squash in the fall. I can’t wait to get in the kitchen this weekend and hopefully spend some time baking a few pumpkin recipes!! Have a fabulous weekend!

  4. Reposted from Yummly where I fund this recipe (and your blog).
    In my opinion, this recipe is great, especially as a perfect muffin to eat for breakfast. The process is a little tedious, but the recipe is forgiving and even adjustable. I used spelt flour instead of whole wheat, used a combination of cinnamon, allspice, nutmeg, ground ginger and cloves just enough to fill 1 tsp instead of pumpkin spice and mashed the roasted butternut squash I had with my hands instead of using the food processor. I also accidentally mixed in the milk and butter in with the wet ingredients instead of by themselves in their own steps. I baked them at 350 degrees for abut 30-45 minutes (until a toothpick in the middle came out clean and the top was firm). All of these adjustments were a combination of using what I had and a little forgetfulness.

    So while this review is not on the recipe followed exactly, I do think this makes the recipe even better. Whether you are substituting ingredients or missing a step, the muffins can and probably still will come out very good. If you don’t have butternut squash, pumpkin would work just as well. It is not too sweet, healthy and very filling. Also, I turned it into a dessert by putting cinnamon whipped cream on top like a cupcake. Very moist, satisfying, easy to make and good for you. This is definitely a keeper and thank you for sharing the recipe 🙂

  5. I know this recipe was posted at least a year ago by the comment dates (and I don’t know if you’ll even see this comment) but I just want to say that I LOVE these muffins! We bought a house this year and planted a big garden with 6 squash plants and this is the perfect recipe to use up all it’s yield. I make them at least once a week to keep on hand for a quick breakfast or snack.
    I was wondering if you know how this might turn out as a quickbread? Maybe dropping the oven temp and increasing bake time… but I’m not sure if any other adjustments are in order. We’re doing a Thanksgiving brunch and I’d love to bring this as a loaf if it would work out.
    If you have any input I’d really appreciate it, and if not please just know that these are greatly enjoyed by all of our family and friends!

    1. Thank you, Danielle! I am so glad to hear that you love these muffins – they are one of my favorites also! Baking for 50-55 minutes at 350 degrees should work for making this into a quickbread.

  6. This recipe looks amazing! Can’t wait to try it. Do you think I could use a sugar substitute for the brown sugar? I ask because I’ve essentially cut out sugar but can have small amounts which include rice malt syrup or stevia. Thanks so much!

    1. Hi Stacy! I have not tested the recipe with any sugar substitute; I would recommend avoiding any liquid sugar substitutes, as this is already a pretty wet batter. I think that a sugar substitute with a similar texture to brown sugar would work well, such as stevia or coconut sugar (again, I have not tested either of these, so I am hypothesizing).

  7. These were great! Not too sweet, but not bland either. I cooked mine quite a bit longer and they were still a little raw inside, I’m sure it’s because I swapped the flour though (I used almond flour instead). I think they taste great though!

  8. Made this with mixed veggie puree, because I didn’t have as much squash as I thought. So mine were squash, green bean, carrot, and apple muffins. I used up all the bits of leftover veggies in the fridge plus a fruit and veggie pouch.

    I also used half whole wheat and half all purpose flour because I wanted the 3 year old to actually consume them.

    She woke up while they were cooling and we split one with butter and honey. These passed the toddler test and she had another one with some milk. (That’s more veggies than she’s had all week, lol).

  9. 5 stars
    I cannot believe that my picky 8 y/o loves these muffins!! So glad I found this recipe to sneak healthy food into her diet! Thank you so much for sharing!

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