Butternut Squash Muffins {Paleo}

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Butternut Squash Muffins are Paleo and Gluten-free and take just 10 minutes to mix up! You’ll love these moist, plump muffins, their perfect texture and just how satisfying they are. Also nut-free.

butternut squash muffins in baking pan

Phasing off GAPS Diet

Don’t you love big muffins: plump, tall, moist and splitting at their seams? Break off a chunk, both crusty and tender. Muffins are my favorite baked good.

After almost five years on the GAPS Diet, our family is phasing off. There have been times in that five years that I didn’t expect ever to be able to say that. But it’s happening; and it’s going well.

Resistant Starch

What foods to introduce first? Well, my answer is foods with resistant starch. Fun foods, yes, foods we’ve been wanting to have, yes, but excitingly, these two are not mutually exclusive.

Foods that contain resistant starch are excellent for one’s gut (once it’s healed and sealed) because they provide food for good gut flora. Another way of saying that is: Resistant starch foods contain prebiotics which feed probiotics.

Yes, cassava flour, the main player in these muffins, contains resistant starch. SO we get to have our cake and eat it too!

We get to eat what we feel excited about introducing into our diet, and it’s good for us!


These muffins don’t have a ton of winter squash in them, just enough to impart moistness and a subtle flavor. This makes them a versatile muffin for everyday.

Tips and Variations

I love them best like this ^^^ … but you can also add scads of fun variations: sprouted nuts, dates, chocolate chips … if you want them to be chunky. See the Variations in Recipe notes if you’d like a few more ideas.

We love to eat these plain. They’re also great topped with butter, butter and honey, or chèvre and honey.

Don’t over-bake them, though, because that will dry them out. Do have fun with ’em!

For those of you who like nutritional information and the extra focus on gut health, see a bit more on that below the recipe…

one butternut squash muffin in pan

5 from 2 votes
Butternut Squash Muffins
Prep Time
10 mins
Cook Time
25 mins
Total Time
35 mins

Butternut Squash Muffins can also be made with canned pumpkin. This recipe is made in the blender, so super fast batter to whip up!

Course: Breakfast, Dessert, Snack
Cuisine: American
Keyword: butternut squash, muffin, paleo
Servings: 6 extra-large muffins or 10 regular size
Calories: 371 kcal
Author: Megan
  • 1 cup cassava flour Otto's preferred
  • 2/3 cup flax seed meal golden preferred
  • 4 eggs
  • 1/3 cup butternut squash cooked, smashed to measure, leftover squash works great (can also use canned pumpkin)
  • 1/3 cup avocado oil or preferred traditional fat, melted
  • 1/3 cup pure maple syrup or honey
  • 2 teaspoons vanilla extract
  • 1 teaspoon cinnamon
  • 1 teaspoon ginger
  • 1/2 teaspoon baking soda , sifted
  • 1/4 teaspoon sea salt
  1. Prepare muffin tin or extra-large muffin tin by lining cups with parchment cut or torn into 6" by 6" squares. Or use muffin liners. (See favorite liners in Recipe notes below.) Preheat oven to 325 degrees Fahrenheit.
  2. In a medium size mixing bowl combine the following dry ingredients: cassava flour, flax seed meal, cinnamon, ginger, baking soda and sea salt.
  3. Place the following wet ingredients in a high-powered blender: eggs, winter squash, oil, maple syrup, and vanilla. Puree until thoroughly mixed, about 15 seconds.
  4. Pour wet pureée into dry ingredients and fold together completely without over-mixing.

  5. Fill prepared muffin cups with batter. Bake extra-large muffins for about 25 minutes. Bake medium/"normal" size muffins about 15 minutes. Muffins are done when toothpick or sharp knife inserted into center comes out clean.
Recipe Notes

Here's my favorite muffin cup liner: it's pretty, doesn't stick at all, and expands slightly for larger muffin cup pans, as needed.

For larger muffins every time, this is the same brand of cup liner, but this liner is deeper and broader, also super pretty.


  • Use canned pumpkin, for convenience, in place of butternut squash.
  • Fold in 1 cup chocolate chips, before baking.
  • Substitute smashed banana or very ripe (black) plantain for the squash.
Nutrition Facts
Butternut Squash Muffins
Amount Per Serving
Calories 371 Calories from Fat 198
% Daily Value*
Total Fat 22g 34%
Saturated Fat 3g 15%
Cholesterol 109mg 36%
Sodium 238mg 10%
Potassium 253mg 7%
Total Carbohydrates 35g 12%
Dietary Fiber 6g 24%
Sugars 12g
Protein 8g 16%
Vitamin A 19.7%
Vitamin C 3.2%
Calcium 11.8%
Iron 14.9%
* Percent Daily Values are based on a 2000 calorie diet.

Cassava Flour

If you have struggled with constipation, I hope you’ll give cassava flour a try. It’s got just enough resistant starch to set your colon into action, without causing gas or too much of a good thing.

Read here about what makes Otto’s the superior cassava flour. The main reasons I buy Otto’s is that it’s non-GMO and they take special precautions to avoid the growth of mold after the yuca are harvested. Enough said, right?two butternut squash muffins in pan

Comments 38

  1. I have not yet tried cassava flour, but I’m hearing about it everywhere! These sound so yummy. I love all of the flavors you included in them!

  2. Excited to try Cassava flour and this recipe. I wanted to share, Megan, that I followed the links on the Otto’s site to a Canadian distributor. Just called them. It’s $$ but I did find it.
    Will organize a purchase at some point and make these muffins! Yay!

  3. Good to know that the cassava flour may ease constipation. Some of the people may find it not effective for them. If constipation still bothers you, then take my best reliever of constipation. I have this Digestic from Mimonis which showed its effectiveness by giving back my normal bowel movement.

    1. Not yet, but I love that question, because we have commented while eating various trials (recipe experiments) with the ingredient that it would make GREAT pasta! I can’t wait to try what you come up with!

    2. Lol I can’t either! Day 19 on Whole 30 and I’d kind of like some tortillas…11 more days and even then I want them to be grain free!

  4. Just had to say these are the best “paleo” muffins I have made, ever! Most are just okay & have a strange texture/taste. These are perfect & have such a great, not-too-sweet, mild flavor. The texture is perfect too. So excited! Thanks!

    FYI – here are a couple changes I made just because of what I had available. Instead of avocado oil I used half grass-fed butter & half coconut oil (melted) & Instead of all maple syrup I used half maple syrup & half raw honey.

    1. YAY!!! So glad! Thanks for writing to let me know! I have a muffin passion, and I’m not big on all the almond flour used these days. Yep, those variations are ones I’d make any day of the week, too. 🙂 Hurrah and thanks again for letting me know!

    1. Hi Tina, no it’s the starch that’s taken from the manioc root. Cassava is the whole root. They are different and don’t perform the same way in recipes.

  5. I just finished making these and I’m very pleased with how they turned out! Thank you! For anyone who is curious, here are the changes I made: I tripled the recipe, (18 servings/12 eggs,) and I subbed ghee for avocado oil, sweet potato for butternut, and I after tasting the batter, I added lots more salt, vanilla, and some stevia. (And left out the ginger.) I cooked them in normal-sized muffin tins with silicone liners for 18 min at 325. After tasting the final product, I think they could have used even more salt and sweetener though…haha, but my family likes a lot of salt! I will definitely add these to our muffin rotation! They would be incredible with chopped apples (but we are allergic,) or chopped pecans, or shredded coconut fyi. Thanks! I’m going to try your cassava sandwich bread next!

  6. In your article re: “Which Seeds Should be Soaked” you say: “Simply add 1/4 cup of probiotic food/beverage, and allow the batter to sit out for 4 hours. Then refrigerate overnight or for a couple of days, before scooping it into your muffin tin and baking!”

    1) Would this be true even if I’ve used “Flax eggs” in the batter or would this only work if using real eggs? (I am sensitive to eggs).
    2) Will ACV work in lieu of the dairy products (kefir, yogurt)?

    Thank you

    1. Post

      Hi Tracy, great questions. Unfortunately, this muffin recipe isn’t a good candidate for also using flax eggs. The reason is: If baked goods with eggs have 3 or more eggs, they don’t replace well. 1 or 2 egg recipes work well with flax eggs. Re your second question, I’m so glad you asked that: Yes! ACV will work in batters to ferment the seeds! 🙂

  7. Megan, thank you for your effort to educate us, and help us serve our families better.

    Could I not use the ground flax seeds?

    Could I replace them with somehing else?

    Thank you.

    1. Post

      Hi Carmen, my pleasure. Thank you! Yes, you can use ground flax seeds, perfect. If you want an alternative, you could also try subbing the flax seeds for tiger nut flour, and increasing the fat to 1/2 cup. I haven’t tried this sub, but I think it will work. I’m traveling this week, but when I get home I think I’ll try it too! 🙂

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