These paleo butternut squash muffins are a healthy, gluten free, and nut free breakfast that kids love and moms love to serve. Packed with a classic fall vegetable puree and naturally sweetened with banana, these muffins are the perfect grab-and-go morning treat!
I might have spent a little too much of my precious ‘free time’ trying to perfect these paleo butternut squash muffins. Maybe it’s the type A, OCD-like tenancies I have, maybe I just wanted to get it perfect for all of you, or maybe I’m just a crazy baker lady that talks to her oven. Or just crazy period. I’m not sure.
I wasn’t even planning on sharing this recipe on my site until my kids at ALL FOUR batches of muffins I made (you know, trying to perfect them). That folks, is called a mom win without trying to be super mom. Queue the applause.
If you followed my muffin journey on Instagram stories, you know the problem I had with these babies (and yes, they are babies since I baked them in a mini muffin tin), is that they came out slightly mushy inside the first few attempts. It was driving me bonkers!! I mean, my kids didn’t care, but I couldn’t share a mushy muffin recipe. What kind of food blogger would that make me?!
But I made an executive decision (since I’m kind of the executive here at Physical Kitchness) to post ’em! After I got them juuuuuuust right of course.
Look, if you’re looking for a beautiful breakfast baked good you can share with everyone at the office and have people saying, “Oh my gosh Carol, you need your own baking show!”, then these probably aren’t it. Actually, your name is probably more like Jessica or Sarah or Kristie anyway…#childrenofthe80’s
But if you’re looking for a breakfast treat that is sweetened naturally with banana and a pinch of pure maple syrup, that the kids will love, and you’ll feel like Daniel Tiger’s mom serving (that tiger lady is perfection), this is your muffin. It’s basically like feeding the little ones veggies for breakfast. IS THAT EVEN POSSIBLE?! Yes, yes it is. And they’ll like it. Truly. I could have played around to lessen the squash and add other components to these paleo butternut squash muffins aim for perfect texture, color, buoyancy (is that term even used in baking?), and visual appeal, but my goal was VEGGIES. Kids consuming veggie overrules any prior logic or rational thinking. Am I right?!
These paleo butternut squash muffins have a super moist center, making it a great option for even itty bitty ones (like my 14-month-old, still with only 4 teeth). And they’re gluten free, dairy free and nut free. Allergy moms of the world – I got your back!!
Be sure to skim these notes for some things to keep in mind!
- I used the canned butternut squash from Trader Joe’s. If you’re grocery store has canned butternut squash, DO THIS. It saves so much time! You could certainly roast your own butternut squash and puree as well
- Cook time may vary, but typically 30 minutes is the golden ticket. If the muffins still haven’t ‘set’ after 30 minutes, keep them in another 5-7 minutes or so
- I tried these baked in a mini muffin tin (featured in these photos) and a normal-sized muffin tin. The mini tin seems to be better, since the muffins cook more throughout the center. Although I should note, the baby loved the mushier ones in a regular muffin tin! Get the mini muffin tin I used HERE.
- These muffins are not overly sweet. If you think you need to add a little more sweet to these veggie-loaded, bite-sized baked goods, add more maple syrup to taste
- You can sub the eggs for a chia egg or flax egg replacement
In need of more healthy ideas the kids will love? Be sure to check out the “Toddler Approved” category in my recipes. To view, click HERE.
PrintPaleo Butternut Squash Muffins

Ingredients
- 15 ounces butternut squash puree
- 1 ripe banana
- 1 tablespoon pure maple syrup
- 2 eggs
- 3/4 cup tapioca flour
- 1/2 cup coconut flour
- 1 1/2 teaspoons baking powder
- 1 teaspoon baking soda
- 1 teaspoon pumpkin spice
- 1/2 teaspoon cinnamon
Instructions
- Preheat oven to 375 degrees
- In a small bowl, combine the tapioca flour, coconut flour, baking powder, baking soda, pumpkin pie spice, and cinnamon
- In a separate mixing bowl, combine the butternut squash puree, banana, maple syrup, and eggs. Mix until combined
- Next, slowly add the dry ingredients to the wet ingredients, beating on low using an electric mixer – just until combined. Do not over-mix
- Spray a mini muffin tin with oil and scoop one heaping tablespoon of the muffin mixture into each mold. The molds should be roughly 3/4 full
- Place the mini muffin tin into the oven and bake for 30-35 minutes
- Let the muffins cool for 5 minutes in the tin then gently remove and cool on a wire rack
Disclaimer: Please note that there are affiliate links on this page and I will earn a small commission if you purchase through those links. However, all opinions are my own. Thank you for your support.

Thank you for this recipe. I have an 18 month that just decided she hates breakfast. These look like the perfect thing to trick her with!
She’ll be so deceived 😉
Do you think you could sub in acorn squash? Asking because I have half a cooked one in my fridge! These look so yummy!
Yep!!
what would you say the serving size is on these? Thanks
It should yield around 24 mini muffins
I’d much rather have a baked good that is simple and delicious and packed full of yumminess like this one, because it’s so fun to try baked goodies from my friends, knowing that you spent a lot of time developing the recipe. <3
You are the baking queen too!
Ok, I’ve made these muffins 3x’s this week and still can’t get enough!
First time they were really mushy (I used a regular muffin tin), still delicious! I also used tin liners cuz I was feeling lazy about cleaning the pan after (horrible idea) they stuck to the papers. Second time I made them mini and they were so good! Although impossible not to eat 8 in one sitting (it’s like a handful if popcorn, right?)
I even gave two to one of the kids I work with who has autism spectrum disorder and has had terrible food aversions and HE GOBBLED THEM UP! I was in total shock. This is a kid who only eats graham crackers and Oreos for snack!
Last batch I made both mini and regular sizes and cooked the bigger ones for a few minutes longer and they were perfect! Everyone I’ve shared with has raved about how good they are! HIGHLY RECOMMEND THESE!!!
(It won’t let me rate these 5 stars for some reason but I definitely would!!)
★★★★
Awe Lindsey – your feedback is so awesome. THANK YOU! So happy to hear they were a hit!
I made these and they are delicious. I didn’t have the tapioca flour so I used almond flour and it worked great. Mine were a little mushy in the center but I think I should have let them bake longer. Honestly though, I like them a little mushy in the center. So good I am making again this afternoon! Thanks for another great recipe!!! You made following my Whole30 and then transitioning to a paleo diet so simple and delicious for me! And your sense of humor is just a bonus! Thank you for being you!
★★★★★
Thanks for the feedback and the sweet comment Michelle!
Question. I don’t have coconut flour in the pantry. Do u know offhand if almond flour would work?
This recipe is pretty finicky (can easily stay mushy in the center) so I felt like coconut flour really helped soak up the moisture from the butternut squash. I’m not sure I would try it but if you do, let me know!
Do you know the caloriecount on a regular size muffin? I am doing my fitness pal. Thanks.
I’m sorry, unfortunately I don’t!
I have an allergy to bananas. Any idea what I could substitute for the banana?
TIA!
Try omitting completely and sweetening more with maple or honey!
My 4.5, 3yo and 15mo just ate an entire batch in two days! And I didn’t feel bad about it because veggies! Thanks so much!
★★★★★
ROCK ON! Love it!