Cinnamon Gluten-Free Butternut Squash Muffins

I used to think gluten-free baking was this complicated thing that required a dozen different flours and a science degree. Every time I tried to make something without regular flour, it turned out dense and crumbly. My kids would take one bite and politely ask for regular muffins instead.

Then I discovered that butternut squash is basically a secret weapon for gluten-free baking. It adds natural moisture and sweetness, so you don’t need all those fancy ingredients. These muffins come out soft and fluffy, and my family actually asks for seconds. Sometimes the simplest solutions are right there in your produce aisle.

What Kind of Butternut Squash Should I Use?

You can absolutely use store-bought butternut squash puree for these muffins – it’s convenient and works perfectly well. If you want to make your own, look for a butternut squash that feels heavy for its size and has a tan, matte skin without any soft spots or green streaks. When making fresh puree, you’ll roast the squash halves cut-side down until they’re fork-tender, then scoop out the flesh and blend it smooth. Whether you go homemade or store-bought, make sure your puree is thick and not watery, as too much moisture can make your muffins dense instead of fluffy.

Options for Substitutions

These gluten-free muffins are pretty adaptable, but there are a few key ingredients you’ll want to keep as-is:

• Coconut flour and tapioca flour: These two flours work together to create the right texture, so I’d recommend sticking with them. If you absolutely need to substitute, try almond flour (use ¾ cup) plus arrowroot starch instead of tapioca, but the texture will be different.
• Butternut squash puree: Pumpkin puree works perfectly as a 1:1 swap. Sweet potato puree also works well, though it’ll give a slightly different flavor. Make sure any substitute is thick, not watery.
• Coconut oil: You can use melted butter or avocado oil instead. If using butter, let it cool slightly before mixing with the eggs to prevent scrambling.
• Maple syrup: Honey works as a direct substitute, or you can use agave nectar. For the maple sugar in the topping, brown sugar or coconut sugar will work just fine.
• Pecans: Walnuts, chopped almonds, or even pumpkin seeds make great substitutes in the topping. You can also leave them out completely if you prefer plain muffins.
• Baking powder: Make sure to use grain-free baking powder to keep these truly gluten-free. Regular baking powder often contains cornstarch, which some people avoid on grain-free diets.

Watch Out for These Mistakes While Baking

The biggest mistake with gluten-free muffins is overmixing the batter, which can make your muffins dense and gummy instead of light and fluffy – mix just until the ingredients are combined and no dry flour is visible. Since coconut flour is super absorbent, make sure your butternut squash puree isn’t too watery by draining it well or roasting your squash cut-side down to avoid excess moisture that can make the muffins soggy. Don’t skip letting the batter rest for 5-10 minutes before baking, as this gives the coconut flour time to fully hydrate and creates a better texture. For perfectly domed muffins, fill your liners only about 2/3 full and avoid opening the oven door during the first 15 minutes of baking, which can cause them to collapse.

What to Serve With Butternut Squash Muffins?

These muffins are perfect for breakfast or an afternoon snack with a hot cup of coffee or chai tea – the warm spices really complement those cozy fall flavors. I love serving them alongside a simple fruit salad with apples and pears, or even just sliced bananas with a drizzle of almond butter for extra protein. For a more indulgent treat, try warming them up and spreading a little butter or cream cheese on top, which pairs beautifully with the sweet butternut squash and maple flavors. They’re also great packed in lunchboxes or enjoyed as a quick grab-and-go breakfast with a glass of milk or your favorite plant-based milk alternative.

Storage Instructions

Keep Fresh: These muffins stay moist and delicious when stored in an airtight container at room temperature for up to 3 days. Since they’re made with coconut flour, they actually get better after sitting for a day as the flavors meld together nicely.

Refrigerate: For longer storage, pop them in the fridge where they’ll keep fresh for up to a week. The butternut squash keeps them naturally moist, so they won’t dry out like some gluten-free baked goods tend to do.

Freeze: These muffins freeze really well for up to 3 months! Wrap each one individually in plastic wrap or store them in a freezer-safe container with parchment paper between layers. Perfect for grabbing a quick breakfast on busy mornings.

Warm Up: To enjoy frozen muffins, just thaw them at room temperature for about 30 minutes or pop them in the microwave for 20-30 seconds. If you want that fresh-baked taste, warm them in a 300°F oven for 5-7 minutes.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 820-890
• Protein: 15-18 g
• Fat: 48-55 g
• Carbohydrates: 90-100 g

Ingredients

For the muffin batter:

• 3 large eggs
• 1/4 cup maple syrup
• 3 tbsp coconut oil
• 1/2 cup butternut squash puree
• 1 tsp vanilla extract
• 1/4 cup coconut flour
• 2 tbsp tapioca flour
• 1/8 tsp fine sea salt
• 1 tsp grain-free baking powder
• 1/2 tsp ground cinnamon
• 1/8 tsp grated fresh nutmeg

For the pecan topping:

• 2 tsp maple sugar
• 1 tsp maple syrup
• 1/4 cup chopped pecans
• 2 tsp tapioca flour
• 1 tsp coconut oil
• 1/8 tsp ground cinnamon
• Pinch sea salt

Step 1: Roast and Puree the Butternut Squash

• 1/2 cup butternut squash puree

Preheat your oven to 400°F.

Cut the butternut squash in half and drizzle it with olive oil to coat.

Place the squash halves face down on a baking sheet and transfer to the oven.

Roast until the squash is tender, about 25 to 30 minutes.

Remove the baking sheet from the oven and let the squash cool enough to handle.

Scoop the flesh out and blend or process in a blender or food processor until smooth.

Refrigerate the puree in an airtight container until you need it for the muffins.

I always make extra puree to keep on hand for soups or other baked goods.

Step 2: Make the Muffin Batter

• 3 large eggs
• 1/4 cup maple syrup
• 3 tbsp coconut oil
• 1/2 cup butternut squash puree (from Step 1)
• 1 tsp vanilla extract
• 1/4 cup coconut flour
• 2 tbsp tapioca flour
• 1/8 tsp fine sea salt
• 1 tsp grain-free baking powder
• 1/2 tsp ground cinnamon
• 1/8 tsp grated fresh nutmeg

In a large bowl, combine the eggs, maple syrup, melted coconut oil, 1/2 cup of the prepared butternut squash puree (from Step 1), and vanilla extract.

Sift the coconut flour, tapioca flour, fine sea salt, grain-free baking powder, ground cinnamon, and grated fresh nutmeg into the wet ingredients.

Whisk until the batter is fully incorporated and smooth.

For a slightly spicier muffin, I like to add a pinch more cinnamon.

Step 3: Fill Muffin Cups and Prepare Topping

• batter (from Step 2)
• 2 tsp maple sugar
• 1 tsp maple syrup
• 1/4 cup chopped pecans
• 2 tsp tapioca flour
• 1 tsp coconut oil
• 1/8 tsp ground cinnamon
• pinch sea salt

Line a muffin tin with six paper liners.

Divide the prepared batter (from Step 2) evenly among the liners.

Set the muffin tin aside while you prepare the pecan topping.

In a small bowl, mix together maple sugar, maple syrup, chopped pecans, tapioca flour, coconut oil, ground cinnamon, and a pinch of sea salt.

Sprinkle this mixture generously over each filled muffin cup.

Step 4: Bake and Cool the Muffins

Bake the muffins in the preheated oven at 400°F for 18-20 minutes, or until a toothpick inserted in the center comes out clean.

Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely.

I like to enjoy these muffins warm with a touch of extra maple syrup drizzled on top.

Cinnamon Gluten-Free Butternut Squash Muffins

Delicious Cinnamon Gluten-Free Butternut Squash Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 19 minutes mins

Cook Time 38 minutes mins

Total Time 57 minutes mins

Servings 4

Calories 855 kcal

Ingredients

  

For the muffin batter:

• 3 large eggs
• 1/4 cup maple syrup
• 3 tbsp coconut oil
• 1/2 cup butternut squash puree
• 1 tsp vanilla extract
• 1/4 cup coconut flour
• 2 tbsp tapioca flour
• 1/8 tsp fine sea salt
• 1 tsp grain-free baking powder
• 1/2 tsp ground cinnamon
• 1/8 tsp grated fresh nutmeg

For the pecan topping:

• 2 tsp maple sugar
• 1 tsp maple syrup
• 1/4 cup chopped pecans
• 2 tsp tapioca flour
• 1 tsp coconut oil
• 1/8 tsp ground cinnamon
• pinch sea salt

Instructions

 

• Preheat your oven to 400°F. Cut the butternut squash in half and drizzle it with olive oil to coat. Place the squash halves face down on a baking sheet and transfer to the oven. Roast until the squash is tender, about 25 to 30 minutes. Remove the baking sheet from the oven and let the squash cool enough to handle. Scoop the flesh out and blend or process in a blender or food processor until smooth. Refrigerate the puree in an airtight container until you need it for the muffins. I always make extra puree to keep on hand for soups or other baked goods.
• In a large bowl, combine the eggs, maple syrup, melted coconut oil, 1/2 cup of the prepared butternut squash puree (from Step 1), and vanilla extract. Sift the coconut flour, tapioca flour, fine sea salt, grain-free baking powder, ground cinnamon, and grated fresh nutmeg into the wet ingredients. Whisk until the batter is fully incorporated and smooth. For a slightly spicier muffin, I like to add a pinch more cinnamon.
• Line a muffin tin with six paper liners. Divide the prepared batter (from Step 2) evenly among the liners. Set the muffin tin aside while you prepare the pecan topping. In a small bowl, mix together maple sugar, maple syrup, chopped pecans, tapioca flour, coconut oil, ground cinnamon, and a pinch of sea salt. Sprinkle this mixture generously over each filled muffin cup.
• Bake the muffins in the preheated oven at 400°F for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely. I like to enjoy these muffins warm with a touch of extra maple syrup drizzled on top.