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Butternut Squash Muffins

Butternut Squash Muffins – These pillowy soft and sweet Butternut Squash Muffins are made with roasted butternut squash and deliciously healthy! Gluten free, dairy free and naturally sweetened with coconut sugar (or dates). In less than 30 minutes, you can make a batch of these muffins to serve to hungry teenagers or for a quick make ahead breakfast.

Add in mini dairy free chocolate chips, raisins, chopped walnuts or hemp hearts to increase the overall nutrient profile.

Grab a Butternut Squash, Roast it and Make Butternut Squash Muffins

Butternut squash is bursting with anti-aging and anti-inflammatory nutrients. So, naturally we have lots of recipes with butternut squash. I will share a bit about the nutrition benefits, how to cut, how to bake and some of my best recipes with butternut squash.

Butternut squash is incredibly easy to roast – just turn on your oven to 400 degrees. Cut your squash in half, scoop out the seeds and season with olive oil and sea salt. Roast for about 25-35 minutes until a fork easily depresses the pulp.

Let’s talk about non-toxic muffins pans for a minute…

Swap Your Muffins Tins for 100% Ceramic Non-Toxic Muffins Pans

A few months ago I started using the Xtrema Cookware new Muffins Pans and WOW! With just a little coconut oil, everything I bake pops out without hesitation. No scrapping or picking required!

Consider swapping your muffins tips for 100% non-toxic muffin pans. Aluminum and other metals can leach into your food and the non-stick pans and ceramic-coated pans are even worse! Ick. If you’re looking for a place to start this Xtrema 6 Standard Muffin Pan is a good go-to in my kitchen plus you can save an extra 15% off by using our exclusive code: CCX15 with your order.

butternut squash muffins

How to Make Perfect Butternut Squash Muffins

The idea to mix butternut squash in a muffin was inspired by Jessica Seinfeld’s Deceptively Delicious cookbook. Jessica gives strategies for hiding nutritious food in tasty meals fit for kids.  In her book, her recipe for “Applesauce Muffins” uses 1/2 a cup of butternut squash puree, which I thought was a great idea!

Unfortunately, her recipe still uses refined sugar, milk (how we feel about dairy), margarine, vegetable oil and refined flour. Yikes! Although this recipe is definitely not as healthy or anti-inflammatory as we would like it to be. That said, Jessica is a genius for forwarding this trend of hiding deliciously nutritious foods in her children’s foods.

With older kids now, we don’t do any hiding — instead we playing a guessing game. “What is in that dish you’re eating?” And then they get to guess which vegetable is enjoyed without knowing it!

Consider These Healthy Butternut Squash Muffin Ingredients:

We want to follow her lead and take it a step further by giving Jessica’s muffins a Clean Cuisine makeover by doing the following:

  1. Use gluten free flour and almond flour instead of refined flour (learn more about white whole wheat flour HERE)
  2. Naturally sweeten our muffins with coconut sugar or organic pitted dates and ripened banana
  3. Using organic, pastured eggs instead of conventional eggs
  4. Add a lot more butternut squash – use 1 1/2 cups of roasted butternut squash or 10oz of frozen squash thawed out
  5. Swapping nutrient-rich organic extra virgin coconut oil for the vegetable oil

Now, let’s make some deliciously healthy butternut squash muffins!

butternut squash muffins

Butternut Squash Muffins for the Win!

Okay, okay… yes, this is less of a makeover and more of a complete re-do of the recipe. But, I got the idea for adding butternut squash to my muffins from Jessica’s recipe.

And, I frequently think of her book when I’m looking for ways to add more vegetables to recipes.

Like adults, kids absolutely LOVE these muffins, by the way. What is so spectacular about these Butternut Squash Muffins is how pillowy soft and super moist they turn out. Plus, they have the perfect amount of sweetness – a delicious fall fix.

They are Butternut Squash Muffins are “anytime muffins”—great for breakfast, lunch, snack, or even as a dinner muffin!

butternut squash muffins

We Love Coconut Butter Slathered on these Butternut Squash Muffins

Have you ever used Coconut Manna before? If not, you’re in for a real treat. Especially if you spread this on top of recipe for Healthy Pumpkin Muffins. Better than butter and loaded with super healthy nutrients… but also delicious!

I have seen Nutiva Coconut Manna locally at our Whole Foods Market and natural foods store, but the cheapest place I have found it is online either at Thrive Market or

butternut squash muffins

Make Ahead Breakfast by Doubling the Batch!

I am a big fan of making double batches around here to stretch through 1 meal plus a few days of snacks. Just this like this recipe for Butternut Squash Muffins, you don’t have to hesitate saying yes to your kids… or to yourself. Make them ahead of time and enjoy them for a few days. Try these other healthy quick bread recipes that easily double!

  • Blueberry Lemon Loaf – This Blueberry Lemon Loaf offers a subtly sweet and perfectly moist breakfast, snack, or dessert option! Loaded with fresh, wild blueberries, and topped with a sweet yet tart lemon glaze, this bread is one the whole family will love! This recipe can easily be made into muffins!
  • Recipe for Zucchini Muffins – If you’re looking for the perfect make ahead breakfast that is both nutrient dense and satisfying, try this recipe for Zucchini Muffins.
  • Recipe for Healthy Pumpkin Muffins – Fluffy, moist and perfectly delicious, try this recipe for Healthy Pumpkin Muffins. And make a double batch, if you can. Because once your family gets a hold one, they won’t be able to stop eating them.
  • Cinnamon Bun Recipe – This is the best and healthiest homemade cinnamon bun recipe ever! If you are looking for a healthy alternative to the traditional cinnamon roll recipe, then this is it.
  • Vegetable Frittata – Our delicious Vegetable Frittata is made with asparagus, leeks and dill. It’s perfect for brunch but also makes a delicious meatless dinner entree.

Butternut Squash Muffins

Pillowy soft and sweet Butternut Squash Muffins are made with roasted butternut squash and deliciously healthy! Gluten and dairy free.

butternut squash muffins
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  • Prep Time: 15 minutes
  • Cook Time: 22 minutes
  • Total Time: 37 minutes
  • Yield: 810 1x



  1. Preheat the oven to 350 degrees and 10 muffin cups with coconut oil or unbleached parchment liners.
  2. In a high speed blender, add the eggs, butternut squash, coconut sugar or dates, water, banana, coconut oil, lemon juice and vanilla. Process until smooth and creamy. Set aside.
  3. In a large mixing bowl, combine the gluten free flour, almond flour, baking powder, baking soda and sea salt with a stainless steel whisk.
  4. Next, slowly pour the wet ingredients in with the dry ingredients and use a spatula to scrape all of the wet ingredients from the blender container. Using a wooden spoon, combine ingredients until well blended. If using, stir in the raisins and/or chocolate chips.
  5. Using a 3 tablespoon batter scoop, divide the batter among the muffin cups and place in the oven. Bake for 22-26 minutes, or until a toothpick inserted in the middle comes out dry.
  6. Remove from oven and let cool for 10 minutes before serving.

Last Step! If you loved our recipe, leave us a review below. This helps future recipe makers and ensures continued high-quality recipes for years to come!

© 2024 clean cuisine Recipe by:

Aimee Niedosik

Aimee loves to craft delicious, nutrient-dense recipes to share with her family and friends. While in remission from autoimmune diseases and underlying viruses, she still maintains an anti-inflammatory and anti-aging diet. Aimee is a Christian, website designer, autoimmune community leader and lives in North Carolina with her husband, 2 kids and 2 dogs.

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Monday 30th of October 2023

I made these muffins using fresh butternut squash which I had frozen and they turned out great! I had cut up cubes of uncooked butternut squash which I had in the freezer. I unthawed the butternut squash and then roasted it at 400 degrees for 15 minutes and then made the muffins according to the recipe. They are delicious!

Aimee Niedosik

Tuesday 31st of October 2023

Oh yes Jessica -- these are a HUGE hit with our kids and they don't have a clue how healthy they actually are!! Enjoy!

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