Spiced Butternut Squash Muffins

Love pumpkin muffins, but want to switch things up every once in a while? These Spiced Butternut Squash Muffins are the muffins for you! They’re a little milder than pumpkin muffins, but with all the great fall flavor and sweet, moist muffin goodness. Plus, they’re 100% whole wheat and won’t put you into a sugar coma! I originally published this recipe way back in 2010, but it has received a photo update and I thought it deserved to be re-shared. So, enjoy!

These Spiced Butternut Squash Muffins are the perfect healthy fall treat - moist and fluffy, yet oil-free and 100% whole wheat! Great for make-ahead breakfasts or an easy snack!

If you’ve never used butternut squash in a non-savory recipe before, you’re in for a big treat with this muffin recipe! I love the mild, sweet flavor of butternut squash – and it doesn’t disappoint when mixed with warm spices, nutty flax, and tart dried cranberries.

These Spiced Butternut Squash Muffins are the perfect healthy breakfast for a chilly fall morning! They're oil-free, whole wheat, moist & fluffy, and super easy to make.

The butternut squash and mashed bananas keep these muffins moist, and the whole wheat pastry flour keeps them light and fluffy. Make sure you pick up whole wheat pastry flour, not regular whole wheat flour! It’s ground much finer than regular whole wheat flour, so it doesn’t make your muffins dense and grainy :)

These Spiced Butternut Squash Muffins are the perfect healthy fall treat - moist and fluffy, yet oil-free and 100% whole wheat! Great for make-ahead breakfasts or an easy snack!

If you can find canned butternut squash puree, buy it and save yourself some time! Or, you can cut a butternut squash in half and roast it flesh side down at 350 for about 45 minutes, then puree all the flesh and use it for soup, these muffins, and anything else where you want a milder winter squash flavor than pumpkin!

Butternut Squash - the perfect winter squash for light and mild fall muffins! Get the best butternut squash muffin recipe at!

These muffins make your whole house smell like fall while they bake, which is a big bonus. They definitely top my list of favorite muffins for a cozy weekend breakfast (or make-ahead breakfast for any day of the week)!

These Spiced Butternut Squash Muffins are the perfect healthy fall treat - moist and fluffy, yet oil-free and 100% whole wheat! Great for make-ahead breakfasts or an easy snack!

Here’s the full recipe:

Yields 12 muffins     adjust servings

Spiced Butternut Squash Recipe

Prep Time 5 minutes Prep Time
Cook Time 25 minutes Cook Time
Total Time 30 mins Total Time




  • 1.5 C whole wheat pastry flour
  • 1/2 C brown sugar
  • 1/3 C finely ground flaxseed
  • 2 tsp pumpkin pie spice
  • 1/2 tsp salt
  • 1/2 tsp baking soda


  • 1 C pureed butternut squash (canned or fresh)
  • 1/2 C dried cranberries (or chocolate chips)
  • 1/2 C milk or nondairy alternative
  • 2 small very ripe bananas, mashed
  • 1 egg


Preheat oven to 350.

Mix dry ingredients together in one bowl, and wet ingredients together in another bowl. Add wet ingredients to dry and stir until just combined. 

Spoon the mixture into a non-stick or paper-lined muffin tray. Sprinkle with raw oats to make them look pretty, if you'd like!

Bake for about 25 minutes, until a knife comes out clean. 



They’re absolutely perfect with a cup of coffee on a chilly morning!

These Spiced Butternut Squash Muffins are the perfect healthy breakfast for a chilly fall morning! They're oil-free, whole wheat, moist & fluffy, and super easy to make.

Looking for more fall baking recipes? Here are some of my favorite breads, muffins, and treats for chilly days!

Have you ever baked with butternut squash? 


  1. 1

    That sounds like a fantastic (early) birthday weekend. Have fun! :)

  2. 2

    I have all the ingredients for these!!

    And I’m slightly envious of your weekend – how fun!

  3. 3

    Yay for visits back to DC! Happy early birthday – hope you have a great weekend!! :D

  4. 4

    You always have the COOLEST recipes!!! And have an amazing weekend!!! make it a birthday WEEK!

  5. 5

    Hi Anne! Happy Early Birthday! Mine’s actually today… September babies are definitely the best! Have a wonderful birthday weekend!

  6. 7

    28 is still a baby. You look great HAPPY EARLY BIRTHDAY

  7. 8

    I’ll be in DC on Friday night with Emily!

  8. 10

    Delicious looking muffins! Love the idea of using butternut squash…perfect for fall!

  9. 11

    Happy early birthday! Another fannetastic recipe that I can’t wait to try! I haven’t seen canned squash but I’ll have to pay attention for it!

  10. 12

    Oh. my. gosh. these look SOOO good! I need to make them ASAP. The perfect fall treat!

    I’m driving to DC this weekend too! I think I’m going for a running tour of the city on Saturday morning if you care to join, but it looks like you’re busy!! :) (not that I haven’t seen it before, but it’s always fun to see it again)

    Happy early birthday!

  11. 13

    These look great–I love all the fall recipes. Have a safe trip to DC!

  12. 14

    And my birthday is Monday! Happy (early) Birthday!

  13. 15

    Have a great weekend! These muffins look delicious.

  14. 16

    Amazing recipe, as always. Have a great time in DC!

  15. 17

    Happy early birthday! Have a great trip!

  16. 18

    Those look awesome.
    And what a fun birthday weekend you have ahead of you! Safe travels !

  17. 19

    Hey these look great. I just have a question- do you think I could use stevia instead of sugar? (I’m a poor college student and trying to use only ingredients I have on hand to make things).


  18. 21

    Have a great Bday weekend! :)

  19. 22

    I’ve made the “regular” vs “Pastry” mistake so many times, haha. Must. Learn!

    So jealous of your roadtrip to DC!! I’d love to come hop on that trail with you! Enjoy the weekend birthday girl :)

  20. 23

    Spiced butter nut squash?!?! Must try. I stole your idea of using oats to top breads and muffins because it makes them look so pretty.

  21. 24

    oooh talk about tasty!!!!

  22. 25

    Ooh, I have a can of butternut squash puree that I don’t know what to do with. Perfect.

    Happy early b-day!

  23. 26
    Jen Robinson says

    What is the difference in pastry vs. regular flour? And how does it affect the outcome of the recipe?

    • 27

      Whole wheat pastry flour makes for a much lighter, fluffier muffin/bread. If you sub it out for regular whole wheat flour in my recipes, you will end up with a very dense, heavy, gummy muffin. Boo!

      • 28
        Jen Robinson says

        That MIGHT explain the disaster that was my first attempt at your banana muffins… haha! i may need to invest in pastry flour… Do you know why, like scientifically/chemically, it makes a difference?

        • 29

          Lol Jenny!!! That would absolutely be why they were a disaster. I’m not sure why scientifically… don’t ask me questions like that until I’m done with school :) My guess would just be that it’s a much denser, heavier flour though!

  24. 30

    Those muffins look delicious! Just found you playing Foodbuzz food project roulette – so many food blogs, not enough time! :D

    Have a great lunch with your grandma!

  25. 31

    those are preetttyyyy… i have all the ingredients and i might make them this weekend!!! cute blog!!

  26. 32

    Enjoy what sounds like it will be a great weekend. Hope the weather cooperates for you!

  27. 33

    Our couches have the same pillows! We’ve had them for almost 3 years and we’re doing a living room make over and the pillows are about to go but the couches have held up well so we’re keeping them.


  28. 34

    I need to add some squash to my muffins! Im such a terrible baker, but if I find easy enough recipes Im willing to give it a go!

  29. 35

    These look awesome. Thanks for sharing them with us. And enjoy the weekend…

  30. 36

    They sound incredible!

  31. 37

    i love your muffin recipes! how do you think these would do if i subbed out the egg and instead used a little more banana/squash or even applesauce? i really want to vegan-ize these!

  32. 39

    I happen to have a butternut squash at home, so these sound like the perfect use for half of it! Hello baking on Sunday. :) Thank you, Anne!

  33. 47

    Have you ever tried to “grind” white whole wheat flour down further in a food processor to get it close to pastry style? I have an over abundance of King Author “white” whole wheat and would like to try to use some of it up in this wonderful recipe? Thoughts from out there??

    • 48

      I haven’t, but often white whole wheat flour is more soft/less dense than regular whole wheat anyway, so I bet it would work in this recipe! Try it and let me know!

  34. 49

    These muffins sound delicious! But I’m having the same issue as Kori. The recipe is not showing up :( I’ve tried Safari and Google Chrome.

  35. 53

    I love butternut squash, I will have to give these a try.

  36. 55

    I picked up a can of butternut squash the other day! I always intend to sue it and then forget!

  37. 57

    these sound so good! do you know of a good way to replace the egg? i’m not sure since flax is used in the dry ingredients.
    i’m almost wondering if i could leave it out, since theres already flax an mashed bananas in it?

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