• Skip to primary navigation
  • Skip to main content
  • Skip to primary sidebar
Bake It Paleo
  • About
  • Recipes
  • Wellness
  • Shop
menu icon
go to homepage
  • About
  • All Recipes
  • By Meal
  • By Diet
  • By Category
  • Wellness
  • Shop
    • Facebook
    • Instagram
    • Pinterest
    • YouTube
  • search icon
    Homepage link
    • About
    • All Recipes
    • By Meal
    • By Diet
    • By Category
    • Wellness
    • Shop
    • Facebook
    • Instagram
    • Pinterest
    • YouTube
  • ×
    Home » Muffins

    Paleo Butternut Squash Muffins (Gluten Free)

    Published: Nov 4, 2022 · by Katie

    Jump to Recipe·Print Recipe

    These paleo butternut squash muffins are made with almond flour, pureed squash, lightly sweetened with maple syrup and loaded with dark chocolate chips. This healthy squash muffin recipe is perfect as a breakfast side, packed in lunches or as an on-the-go snack.

    stack-of-3-mini-squash-muffins

    Muffins have always been one of my go-to breakfast options for the kids. They're easy to make, my children love them and they're a great way to sneak in veggies like zucchini, pumpkin or squash.

    These paleo butternut squash muffins are made with pureed squash. I steamed and blended my own squash, but you can use canned squash too.

    They are also made with a blend of almond flour and tapioca flour, making these gluten free squash muffins.

    Why You'll Love these Butternut Squash Muffins

    Here's what you need to know about these squash muffins:

    • gluten free and grain free - butternut squash muffins made with almond flour
    • paleo friendly - made with minimally processed, real food ingredients
    • dairy free - no milk or butter
    • refined sugar free - sweetened with maple syrup
    • toddler friendly - mini in size (perfect for handling) and free from most common allergens
    • easy to make - a simple, one bowl muffin recipe!
    • soft and tender - these squash muffins have a wonderful texture

    This healthy paleo butternut squash muffin recipe is one of my family's favorites! You cannot taste the squash, so it's a great way to sneak in a veggie your kids may otherwise not eat.

    paleo-squash-muffins

    Ingredients

    Here's a list of what you'll need to make these paleo squash muffins:

    • pureed butternut squash
    • large egg
    • maple syrup
    • vanilla extract
    • blanched almond flour
    • tapioca flour/starch
    • paleo baking powder
    • baking soda
    • cinnamon
    • salt
    • dark chocolate chips (optional)

    Like mentioned earlier, I cut, steamed and pureed my own butternut squash. However, you may use canned squash if you prefer. Also, any variety of squash should work for this recipe.

    If you need these muffins to be nut-free, then swap the almond flour for tigernut flour. I've tried this swap myself and the recipe works. However, I prefer these muffins made with almond flour (the texture is better).

    ingredients-in-mini-squash-muffins

    How To Make Paleo Butternut Squash Muffins

    These muffins are SO easy! The batter is made in one bowl and these mini squash muffins cook in under 20 minutes. Here's what you need to do:

    First, preheat your oven to 350 degrees F. Grease a mini silicone muffin pan and set aside (I greased mine with avocado oil).

    In a medium-sized mixing bowl, combine pureed squash, egg, maple syrup and vanilla.  Whisk until smooth.

    Add in the almond flour, tapioca flour, baking powder, baking soda, cinnamon and salt.

    Fold the chocolate chips into the batter.

    squash-muffin-batter

    Use a large cookie scoop (2 Tbsp per muffin) to scoop the muffin batter into the mini muffin pan, making 10-11 muffins.

    muffin-batter-in-silicone-baking-pan

    Place the muffins in the oven and bake at 350 degrees F for 16-18 minutes.

    After baking, remove the muffins from the oven and cool them for a few minutes in the baking pan.  Then transfer them to a wire cooling rack.

    freshly-baked-muffins

    Storage

    These mini butternut squash muffins are best stored in the fridge and eaten within one week. You can keep them out on the countertop for a couple days, but because they are preservative free they will spoil more quickly than anything store bought.

    gluten-free-squash-muffins

    More Recipes with Butternut Squash

    • Butternut Squash Brownies
    • Paleo Butternut Squash Bread
    • Butternut Squash Tots

    Enjoy!

    Print
    clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon
    stack-of-3-mini-squash-muffins

    Paleo Butternut Squash Muffins (Gluten Free)

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
    • Author: Katie
    • Prep Time: 5 minutes
    • Cook Time: 16 minutes
    • Total Time: 21 minutes
    • Yield: 10-11 mini muffins
    Print Recipe
    Pin Recipe

    Description

    These paleo butternut squash muffins are made with almond flour and pureed butternut squash.  This healthy muffin recipe is gluten free, dairy free and paleo friendly.


    Ingredients

    Scale
    • ½ cup pureed butternut squash
    • 1 large egg
    • 2 Tbsp maple syrup
    • 1 tsp vanilla extract
    • 1 cup blanched almond flour (90g)
    • ⅓ cup tapioca flour (43g)
    • 1 tsp cinnamon
    • 1 tsp paleo baking powder
    • ¼ tsp baking soda
    • ¼ tsp salt
    • 3 Tbsp dark chocolate chips, chopped (optional)


    Instructions

    1. Preheat oven to 350 degrees F.
    2. Grease a mini silicone muffin pan and set aside (I greased mine with avocado oil).
    3. In a medium-sized mixing bowl, combine pureed squash, egg, maple syrup and vanilla.  Whisk until smooth.
    4. Add in the almond flour, tapioca flour, baking powder, baking soda, cinnamon and salt.
    5. Fold the chocolate chips into the batter.
    6. Use a large cookie scoop (2 Tbsp per muffin) to scoop the muffin batter into the mini muffin pan, making 10-11 muffins.
    7. Place the muffins in the oven and bake at 350 degrees F for 16-18 minutes.
    8. After baking, remove the muffins from the oven and cool them for a few minutes in the baking pan.  Then transfer them to a wire cooling rack.

    Did you make this recipe?

    Share a photo and tag us — we can't wait to see what you've made!

    pinterest image for butternut squash muffins
    « Butternut Squash Tots (Gluten Free)
    Gingerbread Cookie Bars (No Bake, Paleo, Vegan) »

    Reader Interactions

    Comments

    1. Katie

      November 04, 2022 at 6:39 am

      We love these mini squash muffins for snack or breakfast. Hope you all love them too!

      Reply
    2. Haleema

      October 08, 2024 at 7:45 am

      Katie,

      Can these be made in a regular sized muffin pan?

      Reply
      • Katie

        October 08, 2024 at 7:55 am

        They'll bake better in a mini muffin pan, but you can use a regular sized pan if you must.

        Reply

    Leave a Reply Cancel reply

    Your email address will not be published. Required fields are marked *

    Recipe rating 5 Stars 4 Stars 3 Stars 2 Stars 1 Star

    Primary Sidebar

    Hi there!

    I'm Katie and I have a passion for baking healthy treats using real, whole food ingredients. On my blog you'll find a variety of sweet and savory recipes, all gluten free and dairy free. My mission is to make baking nutritious, delicious, simple and family friendly.

    More about me

    Subscribe

    Sign up for my mailing list to get early access to discounts, new recipes and more!

    Subscribe here!

    Cereal

    Cereal is typically anything but healthy... not Lovebird! It's all organic, paleo, plant based AND low in sugar. My kids love it too!

    Lovebird grain free cereal: paleo, vegan and AIP

    Popular

    • Paleo Chocolate Torte (Flourless, No Bake)
    • Healthy s'mores cookies on lined baking sheet.
      Gluten Free S'mores Cookies (Paleo, Vegan)
    • Bite of a brownie protein bite to show texture.
      Brownie Protein Bites (Gluten Free, Paleo)
    • Healthy Coffee Cookie Cups (No Bake, Gluten Free)

    Footer

    ↑ back to top

    About

    • About
    • Privacy Policy
    • Disclaimer
    • Terms & Conditions

    Recipes

    • Paleo
    • Vegan
    • Whole30
    • Nut Free

    Search

    • link to Instagram account
    • link to pinterest account
    • link to facebook

    As an Amazon Associate I earn from qualifying purchases.

    Copyright © 2025 - Powered by Feast+