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Butternut Squash Muffins with Brown Sugar Pecan Topping

Published: Jan 13, 2024 · Modified: Nov 6, 2025 by Great Grub, Delicious Treats · · This post may contain affiliate links

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These butternut squash muffins with brown sugar pecan topping are a scrumptious and delicious fall treat. The muffins are made with roasted butternut squash, and are topped with a brown sugar pecan topping that adds a sweet and crunchy texture to the muffins. They are perfect for breakfast, brunch, or a midday snack.

Six butternut squash muffins stacked on top of each other.

When fall rolls around, everyone gets so excited about pumpkins and apples, but where’s the love for butternut squash? Sure, people roast them for sides, but they forget how delicious they are in baked goods! While I do love to make my share of pumpkin and apple desserts, I’m also a big fan of baking with butternut squash. The flavor of the squash lends itself to all the baked goods that you’d normally make with pumpkin, and just like pumpkin, butternut squash is in season in the fall. One of my favorite ways to bake with butternut squash is making these tasty muffins. They’re tender and moist, and the brown sugar pecan topping really takes them to another level.

Butternut Squash Muffins

These muffins start with a basic muffin recipe that I combine with butternut squash puree to create a muffin flavor that’s similar to pumpkin muffins but a bit more mild. I pour the batter into muffin tins, top it with a simple brown sugar pecan mixture, and bake until the muffins are cooked through and the topping is golden. That’s it! It takes no more time than any other muffin recipe, but the topping gives it a wonderful extra kick of flavor and texture.

A horizontal photo of about 8 muffins of a wood surface with fall leaves in the background.

Why You’ll Love This Butternut Squash Muffin Recipe

  • The combination of the roasted butternut squash, the crunchy, sweet brown sugar pecan topping, and the warm spices is simply irresistible.
  • They are perfect to serve for breakfast, brunch, or a midday snack, and they are easy to make and are so flavorful.
  • These muffins are a great addition during the holidays and make a delicious fall dessert the whole family will enjoy.

Butternut Squash Muffin Ingredients

This muffin recipe uses basic baking ingredients, most of which are probably in your kitchen right now. Anything you don’t have can be found in one quick trip to your local grocery store.

  • All purpose flour
  • Baking powder
  • Baking soda
  • Ground cinnamon
  • Salt
  • Ground nutmeg
  • Ground cloves
  • Ground ginger
  • Pumpkin pie spice
  • Large eggs
  • Butternut squash puree
  • Granulated sugar
  • Light brown sugar, packed
  • Vanilla extract
  • Vegetable oil
  • Brown sugar
  • Chopped pecans
  • Melted butter
A few muffins stacked up on each other.

How to Make Butternut Squash Muffins

Making these muffins is no more difficult than any other muffin recipe. It’s a basic muffin batter, and the topping takes about 5 minutes to mix. Anyone can make these!

Step 1: Prep

Preheat the oven to 350 degrees and line a regular-sized muffin pan with paper liners or spray a muffin pan with nonstick spray.

Step 2: Combine the Dry Ingredients

Whisk the flour, baking powder, baking soda, cinnamon, salt, nutmeg, cloves, ginger, and pumpkin spice together in a medium bowl.

Step 3: Combine the Wet Ingredients

Beat the eggs, butternut squash puree, sugar, brown sugar, vanilla, extract, and vegetable oil together in a large bowl.

Step 4: Make the Batter

Gradually add the dry ingredients into the wet ingredients, beating until well combined.

Step 5: Make the Topping

Combine the brown sugar, flour, chopped pecans, and melted butter in a small bowl.

Step 6: Bake

Fill the muffin tins ⅔ full. Then, top them with the brown sugar pecan mixture and bake for 25 to 30 minutes until a toothpick inserted into the center comes out clean. Enjoy!

A muffin tin with butternut muffins in it after being baked.

Recipe Tips

  • Use room temperature eggs for the best texture and rise.
  • For a lighter texture, let your muffin batter sit for a few minutes before baking.
  • Dark muffin tins will cook the muffins more quickly than lighter colored metal muffin tins.

Variations

  • You can make the topping with chopped pecans, walnuts, or almonds.
  • For ultra-tender muffins, try using cake flour.
  • You can make different muffins by using butternut squash, pumpkin, or sweet potato puree.

What to Serve with Butternut Squash Muffins

These muffins are delicious when paired with a glass of milk or a cup of coffee or tea. You can also serve them with fresh fruit. For a larger breakfast spread, pair these muffins with your favorite savory breakfast options like bacon, eggs, sausage, hashbrowns, pancakes, waffles, and the like.

A close up of a muffin with a bite taken out of it.

Recipe FAQ

What are butternut squash muffins?

Butternut squash muffins are similar to pumpkin muffins. They’re made with butternut squash puree and have a flavor that’s similar to pumpkin but more mellow.

Can I make butternut squash muffins vegan or gluten-free?

You can make a gluten-free version of these muffins by using gluten-free flour. I’m sure there’s a way to make them vegan, but since I’m not vegan, I’m not sure how.

Do butternut squash muffins need to be refrigerated?

Refrigerate these muffins for the best quality.

Can I substitute canned pumpkin puree for roasted butternut squash?

Absolutely. They can be used interchangeably.

Can you freeze butternut squash muffins?

Yes. These muffins freeze very well and will last for up to 3 months when stored properly

A double collage photo of butternut squash muffins.

How to Store Leftover Butternut Squash Muffins

Refrigerate these muffins for up to 3 days in an airtight container. For longer storage, wrap the muffins individually in plastic wrap, then freeze them for up to 3 months in an airtight, freezer-safe container.

Try These Delicious Butternut Squash Muffins Today

These butternut squash muffins are moist, tender, and full of fall flavors like butternut squash, cinnamon, nutmeg, and more. They’re made even better with a sweet and crunchy brown sugar pecan topping. On top of all that, they’re so easy to make, too! You really can’t beat that combination. Give this recipe a try, and I know they’ll be your new go-to muffin recipe for the fall season.

A three photo collage of butternut squash muffins.

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Six butternut squash muffins stacked on top of each other.

Butternut Squash Muffins

Great Grub, Delicious Treats
These butternut squash muffins are moist and delicious, topped with a delicious brown sugar pecan topping, and baked to perfection. The perfect fall dessert the whole family will enjoy.
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Print Recipe Pin Recipe
Prep Time 20 minutes mins
Cook Time 30 minutes mins
Total Time 50 minutes mins
Course Dessert
Cuisine American
Servings 24 Muffins
Calories 230 kcal

Ingredients
  

For the Muffins

  • 2 cups all purpose flour
  • 1 ¼ teaspoon baking powder
  • ½ teaspoon baking soda
  • 1 ½ teaspoon ground cinnamon
  • ½ teaspoon salt
  • ½ teaspoon ground nutmeg
  • ½ teaspoon ground cloves
  • ¼ teaspoon ground ginger
  • 1 teaspoon pumpkin pie spice
  • 4 large eggs
  • 15 ounce butternut squash puree
  • 1 cup sugar
  • ½ cup light brown sugar, packed
  • 1 teaspoon vanilla extract
  • ⅔ cup vegetable oil

Brown Sugar Pecan Topping

  • ¾ cup brown sugar, packed
  • ¼ cup all purpose flour
  • ¾ cup pecans, chopped
  • ¼ cup melted butter

Instructions
 

  • Preheat the oven to 350° and line a muffin pan(s) with paper liners or spray with non-stick cooking spray.

For the Muffins

  • In a medium bowl, whisk together flour, baking powder, baking soda, cinnamon, salt, nutmeg, cloves, ginger and pumpkin spice.
  • In a large bowl, beat eggs, butternut squash puree, sugar, brown sugar, vanilla extract, and vegetable oil together until combined.
  • Gradually add the flour mixture into the wet ingredients, and beat until well combined.
  • Evenly pour batter into muffin pans ⅔ full.

Brown Sugar Pecan Topping

  • In a small bowl, combine brown sugar, flour chopped pecans, and melted butter. Stir well.
  • Top each muffin with the brown sugar pecan topping.
  • Bake for 25-30 minutes or until a toothpick comes out clean.

Notes

Nutritional values are approximate.
 
Please note that these values can change with different brands and any modifications made to the recipe. For the most accurate information, use a nutritional calculator with the exact brands and measurements.

Nutrition

Calories: 230kcalCarbohydrates: 31gProtein: 3gFat: 11gSaturated Fat: 3gPolyunsaturated Fat: 4gMonounsaturated Fat: 3gCholesterol: 32mgSodium: 101mgPotassium: 137mgFiber: 1gSugar: 20gVitamin A: 1985IUVitamin C: 4mgCalcium: 38mgIron: 1mg
Keyword Brown Sugar Pecan Topping, Butternut Muffins, Butternut Squash Muffins
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A stack of muffins on a wood surface.
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Welcome to Great Grub, Delicious Treats! Hello, my name is Terri and I'm so glad you stopped by. I'm a self taught cook/foodie at heart, mom to three kids, photographer and have a love for amazing food. I left my full time job of being a hospice admissions RN, which was super tough and extremely sad, and at times, very rewarding to be there for the patients and families to blog full time which I absolutely love. I hope you enjoy, and check out, all of the delicious recipes on my site while you're here! And don't forget to sign up to receive every new recipe right to your email. Thanks again for stopping by! :)

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Welcome to Great Grub, Delicious Treats! Hello, my name is Terri and I'm so glad you stopped by. I'm a self taught cook/foodie at heart, mom to three kids, photographer and have a love for amazing food. I left my full time job of being a hospice admissions RN, which was super tough and extremely sad, and at times, very rewarding to be there for the patients and families to blog full time which I absolutely love. I hope you enjoy, and check out, all of the delicious recipes on my site while you're here! And don't forget to sign up to receive every new recipe right to your email. Thanks again for stopping by! :) Read More…

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