There's something about rolling cookie dough in cinnamon sugar that feels like kitchen magic. These gluten free pumpkin thumbprint cookies bake up with a crisp, caramelized shell that gives way to a soft, spiced interior and a creamy surprise in the middle.
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Skill Level: Intermediate
Flavor Remix: Swap the cheesecake filling for apple butter or Nutella.
Allergy Watch: Nut-Free
Unlike other pumpkin cookies that can veer toward cakey or overly spiced, this version strikes the right balance.
Think thumbprint cookies-but instead of jam, each little crater holds a sweet, tangy cheesecake filling. They're part cozy fall cookie, part bite-sized dessert plate, and 100% worth making.
The dough itself carries warm pumpkin pie spice, while the coating is just cinnamon and sugar. That little tweak keeps nutmeg and clove from taking over, letting the pumpkin flavor shine.
And here's another secret to success: start with room temperature butter, eggs, and cream cheese so everything whips together smoothly.
Ingredient Notes
- Gluten-Free Flour: Use any 1:1 gluten free flour blend with xanthan gum, like Bob's Red Mill 1:1 Flour or King Arthur Measure for Measure.
- Butter: Use unsalted butter or reduce the salt added by ¼ teaspoon.
- Brown Sugar: I use light brown sugar but dark can be used for a richer flavor.
- Pumpkin: Use canned pumpkin puree, not pumpkin pie filling. Or mash fresh roasted pumpkin.
- Cream Cheese: Full-fat cream cheese makes the filling velvety. Avoid whipped or spreadable styles since they don't set the same.
- Vanilla Extract: Or use vanilla paste.
How to Make Gluten-Free Pumpkin Cookies
A step-by-step visual guide for making gluten-free pumpkin cheesecake cookies. You can skip to the recipe for the full written instructions.
Mix Dry Ingredients
Sifting together the dry ingredients helps them distribute evenly-no surprise clumps of spice.
Cream the Sugar and Butter
Start by creaming butter and sugars together until light and fluffy. This step isn't just for texture-it helps lock air into the dough so the cookies bake up soft rather than dense. When you add the pumpkin and eggs, it will look almost curdled. Don't fret!
Mix the Wet and Dry Ingredients
Combine wet and dry just until no streaks remain.
Chill
Scoop the cookie dough into balls and chill. The chill time keeps the cookies from spreading too much and makes them easier to handle.
Prepare the Cream Cheese Filling
Whisk the filling until smooth and keep at room temp until ready to use.
Roll and Press
Once chilled, roll each dough ball in cinnamon sugar and press a thumbprint-style indentation in the center.
Fill and Bake
Fill with a spoonful of cream cheese mixture, then bake until set at the edges and slightly puffed in the middle. Cooling on the baking sheet first helps them hold their shape before transferring to a rack.
Jen's Recipe Notes
- Always scrape down your mixing bowl after each addition. If butter isn't fully incorporated, it can melt out during baking, leaving the cookies greasy instead of tender.
- You can use a hand mixer or the paddle attachment on a standing mixer.
- Room temperature butter means it is softened to the point that it is easily cut with a butter knife but not liquid.
More Gluten-Free Cookie Recipes
Make Ahead and Storing
Make Ahead: Chill the dough balls for up to 24 hours before rolling in sugar and baking. If you make the cream cheese filling ahead, allow 30 minutes for it to come to room temperature before filling the cookies.
Storing: Keep baked cookies in an airtight container in the refrigerator for up to 3 days.
Freezing: Freeze unbaked dough balls after scooping. Thaw overnight in the fridge before coating in cinnamon sugar and baking.
📖 Recipe
Gluten Free Pumpkin Cookies with Cream Cheese
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Ingredients
- ½ cup unsalted butter room temperature
- ½ cup light brown sugar packed
- 1 cup granulated sugar divided
- ⅔ cup pumpkin puree
- 1 egg room temperature
- 1 teaspoon vanilla extract
- 1 ½ cups 1:1 gluten-free flour with xanthan gum
- 1 teaspoon pumpkin pie spice
- ½ teaspoon kosher salt
- ¼ teaspoon baking soda
- 1 teaspoon cinnamon
Cream Cheese Filling
- 8 ounces cream cheese room temperature
- ⅔ cup granulated sugar
- 2 teaspoons vanilla extract
- ½ teaspoon kosher salt
Instructions
- In a medium bowl, whisk together the gluten-free flour, pumpkin pie spice, salt, and baking soda. Set aside.1 ½ cups 1:1 gluten-free flour with xanthan gum, 1 teaspoon pumpkin pie spice, ½ teaspoon kosher salt, ¼ teaspoon baking soda
- Place the butter, brown sugar, and ½ cup of the granulated sugar in the bowl of a stand mixer fitted with a paddle attachment (or use a hand mixer), and beat on medium-high speed until light and fluffy, about 3 minutes, scraping down the bowl as needed.½ cup unsalted butter, ½ cup light brown sugar, 1 cup granulated sugar
- Add the pumpkin purée and mix until combined. The mixture will look curdled, but that's fine. Mix in the egg and vanilla.⅔ cup pumpkin puree, 1 egg, 1 teaspoon vanilla extract
- Add the dry ingredients (i.e., the flour blend) to the wet ingredients. Mix on low speed until just combined.
- Chill the dough for 1 hour. While the dough is chilling, make the cream cheese filling.
- Preheat the oven to 375°F (190°C).
- Mix the remaining granulated sugar and cinnamon.1 cup granulated sugar, 1 teaspoon cinnamon
- Scoop the cookie dough into 1-inch balls and gently toss them in the cinnamon-sugar mixture. Place the balls about 2 inches apart on your prepared baking sheets.
- Use your thumb to press an indentation into the center of each dough ball, creating a well for the cream cheese filling. Spoon roughly 1 ½ teaspoons of the cream cheese mixture into the center of each indented dough ball.
- Bake for 6-8 minutes, rotating the baking sheet halfway through. Let the cookies cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.
Cream Cheese Filling
- In a medium bowl, mix together the cream cheese, granulated sugar, vanilla extract, and salt until well combined and no lumps remain. Set aside, keeping at room temperature.8 ounces cream cheese, ⅔ cup granulated sugar, 2 teaspoons vanilla extract, ½ teaspoon kosher salt
Equipment
- mixing bowl
- electric mixer or stand mixer
- cookie sheet
Notes
- You can mix the cream cheese filling by hand or use a mixer.
- The dough can be scooped and chilled, or you can scoop it after the chilling.
Nutrition
Recipe Questions
Yes. Use a dairy-free cream cheese (like Kite Hill or Tofutti) and vegan butter substitute. The texture may be slightly softer but still delicious.
Pumpkin adds a lot of moisture. That's why this recipe uses a careful balance of flour and sugar plus a chill step to help set the dough.
Absolutely. The dough makes excellent gluten free pumpkin cookies on its own-just roll, bake, and enjoy.
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