These Butternut Squash Cookies are filled with chocolate chips and toasted pecans, then finished with a classic boiled brown sugar frosting and a whole roasted pecan on top. They're cozy, slightly sweet, and perfect for fall baking or holiday cookie trays.

I first made these cookies after harvesting more butternut squash than usual from our garden. I've baked plenty of squash recipes before, like my Butternut Squash Galette, but this was my first time using it in a cookie, and it was worth it!
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Why You'll Love Butternut Squash Cookies
Soft and tender texture: Butternut squash gives these cookies a cake like softness.
Old-fashioned flavor: The brown sugar frosting adds a nostalgic touch.
Perfect for fall: A great way to use up extra squash from the garden.
Key Ingredients
Butternut Squash Puree: Brings natural moisture and sweetness. Cook and drain squash before using.
Chopped Pecans: Toasted for extra flavor, with whole pecans to garnish the frosted tops.
Semi-Sweet Chocolate Chips: Add rich bursts of chocolate to each bite.
Brown and Granulated Sugar: Used in both the dough and the frosting for deep, sweet flavor.
Butter: Adds richness and helps create a soft crumb.
Substitutions
- Use canned pumpkin instead of butternut squash.
- Swap raisins for the chocolate chips for a more traditional cookie.
- Use walnuts in place of pecans.

Recipe Variations
- Leave the frosting off for a more breakfast style cookie.
- Add warm spices like cinnamon and nutmeg for a cozy twist.
- Make cookie sandwiches with frosting between two cookies.
Top Tips
- It's normal if the batter looks split after adding squash. It smooths out when flour is added.
- Let the squash cool and drain off excess water before using in the dough.
- If the frosting thickens too fast, stir in a splash of milk to keep it spreadable.
Storage
Store frosted cookies in an airtight container at room temperature for up to 3 days, or refrigerate up to 5. Cookies may be frozen for up to 3 months.
Serve With...
Serve these cookies with a glass of cold milk, a cup of hot coffee, or a warm mug of tea. They also make a great addition to lunchboxes, cookie exchanges, or a holiday dessert platter.
More Butternut Squash Recipes
- Butternut Squash Galette
- Cheese Ravioli with Butternut Squash
- Butternut Squash Rolls
- Buddha Bowl with Shrimp and Butternut Squash

When you make this recipe, please comment below and let me know what you think. I'd love it if you tag me on Instagram @grumpyshoneybunch or #grumpyshoneybunch so I can see your photos!
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📖 Recipe

Butternut Squash Cookies with Brown Sugar Frosting
Equipment
- Insulated baking sheet
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Ingredients
FOR THE COOKIES
- ½ cup butter room temperature
- ½ cup brown sugar
- ½ cup granulated sugar
- 1 large egg
- 1½ teaspoons vanilla extract
- ½ cup butternut squash puree
- 1½ cups flour
- ½ teaspoon baking powder
- 1 teaspoon ground cinnamon
- 1 teaspoon salt
- ¼ teaspoon baking soda
- ¼ teaspoon ground allspice
- ½ cup chopped toasted pecans
- ½ cup semi-sweet chocolate chips optional
FOR THE FROSTING
- ¼ cup brown sugar
- 2 tablespoons milk
- 1 tablespoon butter
- 1 cup powdered sugar
Instructions
- Preheat the oven to 350 degrees. In a large mixing bowl, cream together the butter, brown sugar, granulated sugar, egg, and vanilla extract.
- Add the butternut squash and mix until combined.
- In a small bowl, sift together the flour, baking powder, cinnamon, salt, baking soda, and allspice. Gradually add the flour to the squash mixture, stirring until combined.
- Stir in the chopped pecans and chocolate chips (if using)
- Using a small cookie scoop, place cookies 2"apart on a parchment lined cookie tray. Bake for 12 minutes, or until cookie springs back when lightly touched in the center.
- Cool cookies completely on a cooling rack.
- FOR THE FROSTING
- In a large saucepan over medium heat, stir together the milk and brown sugar, bringing to a boil. Boil for 3 minutes. Remove the syrup from heat and add the butter. Stir until melted. Add the powdered sugar and beat until sugar is fully incorporated. The frosting will turn a pale tan color.
- Spread 2 tablespoon of frosting on top of cookies while warm and top cookie with a whole pecan.
Marie B says
Fantastic! Easy to make, tasty, and fluffy! Wonderful way to use butternut squash. Thanks!
Stacee says
These were really yummy but mine ended up flat. Any tips?
Shelby Law Ruttan says
If you followed the recipe exactly and used both the baking powder and baking soda then maybe one of them was too old. Also, did you use fresh or frozen butternut squash? If I have more information I can try to help.