Gluten Free Pumpkin Cheesecake Cookies

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Soft, chewy and swirled with creamy cheesecake filling, these Gluten Free Pumpkin Cheesecake Cookies are the perfect fall treat. They are cozy, decadent and guaranteed to disappear quickly!

Pumpkin cheesecake cookies on white background with one cut in half.

When the leaves start falling and pumpkins start to appear on every porch, there's nothing better than baking up something sweet and seasonal. These Gluten Free Pumpkin Cheesecake Cookies bring together soft pumpkin cookies and creamy cheesecake filling. Each bite has the warm spices of fall paired with that creamy tang we all love in cheesecake just like in my Gluten Free Pumpkin Cheesecake Crumble Bars.

The texture is so irresistible. The pumpkin cookie base is tender, lightly spiced, and just the right amount of sweet. Add in a swirl of cheesecake filling, and suddenly you have a dessert that feels bakery worthy but comes together very easily in your own kitchen.

Looking for more dishes that have pumpkin in them? Try my No Bake Pumpkin Spice Honey Bites, these Gluten Free Pumpkin Chocolate Chip Oat Muffins and this delicious Pumpkin Pie Smoothie.

WHY YOU'LL LOVE MAKING THESE PUMPKIN CHEESECAKE COOKIES

  • Perfect fall treat: Soft pumpkin spiced cookies with a creamy cheesecake swirl center.
  • Simple ingredients: All pantry staples that are easy to source.
  • Crowd pleasing: Enjoy at a holiday gathering or a cozy weekend, they always impress friends and family.
  • Freezer friendly: I can make a batch ahead of time and always have a sweet treat ready to go!

INGREDIENTS + SUBSTITUTIONS

  • Pumpkin puree: Brings natural sweetness, moisture and that signature fall flavor. Use puree pumpkin puree not pumpkin pie filling.
  • White sugar: Adds sweetness and helps create the perfect cookie texture of light and tender.
  • Light brown sugar: Brings a hint of molasses for added depth, warmth and chewiness.
  • Butter: Melted, butter adds richness and helps the cookies bake up soft and flavorful.
  • Egg: Acts as a binder, giving structure while keeping the cookies moist.
  • Vanilla extract: Enhances all the flavors and pairs beautifully with pumpkin and cheesecake.
  • Gluten free 1:1 baking flour: The structure for the cookies.
  • Pumpkin pie spice: A cozy mix of cinnamon, nutmeg, ginger and cloves that instantly gives the cookies that comforting fall flavor.
  • Baking powder and baking soda: These two leavens work together to help the cookies rise and stay soft.
  • Sea salt: Helps balance the sweetness and enhances all the flavors.
  • Cream cheese: The creamy, tangy filling that makes these cookies extra. There's a little bite of cheesecake in the center of each cookies.

Scroll down to the recipe card for quantities used.

Ingredients for the pumpkin cheesecake cookies on white background.

HOW TO MAKE GLUTEN FREE PUMPKIN CHEESECAKE COOKIES

Step 1: In a large bowl, add sugar, brown sugar, pumpkin puree and melted butter. Mix until fully combined. Add in egg and vanilla extract and mix until evenly incorporated.

Bowl with the sugars, pumpkin puree, butter being mixed with the egg and vanilla extract being poured in.

Step 2: In another bowl, add gluten free flour, pumpkin pie spices, baking powder, baking soda and salt, then whisk.

The dry ingredients being whisked in a bowl.

Step 3: Add half of the dry ingredients into the wet mixture and mix until combined. Then add the rest of the dry and mix until combined. Cover with plastic wrap and place in freezer for 1 hour.

The dry cookies ingredients being mixed and combined with the wet ingredients.

Step 4: Add cream cheese, sugar and vanilla to a small bowl and mix until combined.

Cream cheese, sugar and vanilla being mixed in a bowl to make the cream cheese filling.

Step 5: Place parchment paper on baking sheet then using a ½ tablespoon, scoop the cream cheese filling onto the paper making 18 dollops. Cover with plastic wrap and freeze until dough is ready.

Dollop of cream cheese on a baking sheet.

Step 6: Remove cookie dough and cream cheese from freezer and preheat oven to 350 F. Using a cookie scoop, scoop 6 mounds of the cookie dough onto a baking sheet 2-2 ½ inch in diameter and 1 inch thick. Place a cream cheese dollop on the center then cover with a small amount of cookie dough.

The cookie dough on the parchment paper of the baking sheet with a dollop of cream cheese on top.

Step 7: Place cookies into the oven and bake for 18-20 minutes. Repeat until all the dough and filling is used. You can get 18 large stuffed cookies.

The pumpkin cheesecake cookies ready to bake on a baking sheet.

EMILY'S TIPS

  • Use either fresh or canned pumpkin puree. Do not use pumpkin pie filling as it has added spices and sugar that will make these cookies too sweet.
  • Use room temperature cream cheese. Already softened cream cheese ensures the filling is smooth and easy to swirl.
  • Do not overmix the dough. Mix until combined so the cookies stay soft and tender.
  • Chill the dough. Pumpkin adds extra moisture so chilling can prevent spreading.
  • Chill the cream cheese mixture. This prevents it from being too runny when baking.
  • Place a dollop of cream cheese mixture on the cookie dough then swirl and spread before adding another layer of the cookie dough.

SERVING SUGGESTIONS

These cheesecake pumpkin cookies tastes perfect by themselves as a great treat, dessert or afternoon snack. If you are pumpkin crazed like I am this time of year, enjoy with this Pumpkin Pie Smoothie.

As a dessert, a side of Vanilla Honey Ice Cream goes well with these cookies too.

Close up of someone holding a cookie cut in half with remaining cookies in the background.

STORAGE

Refrigerator: Place cookies in an airtight container and refrigerate up to 3-4 days. The cheesecake filling requires them to be store chilled.

Freeze: Place cookies in a single layer on a baking sheet, then transfer to a freezer bag or container for up to 1 month. Thaw overnight in the fridge before serving.

RECIPE FAQ'S

Can I make these cookies dairy free?

Yes! Use a dairy free cream cheese alternative and a plant based butter. You can also use vegetable oil in place of the butter.

Do I need to refrigerate these cookies?

Yes, because of the cheesecake filling, it's best to store them in the fridge.

Can I freeze the cookie dough?

Absolutely! I love doing this! You can freeze the unbaked dough balls (without the cheesecake swirl) and add the filling right before baking.

Can I make these ahead of time?

Yes, these cookies actually taste even better the next day once the flavors meld together.

Can I use pumpkin pie filling?

No, pumpkin pie filling has added spices and sugar. Use only pure pumpkin puree.

Close up of the gluten free pumpkin cheesecake cookie.

I hope you give these Gluten Free Pumpkin Cheesecake Cookies a try! If you do give this recipe a try, please let me know!

Leave a comment with a 5 star rating below. Your reviews and ratings help support Emily’s Wholesome Kitchen and make it possible for me to continue to create the best recipes you know and love.

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Close up of the gluten free pumpkin cheesecake cookie.

Gluten Free Pumpkin Cheesecake Cookies


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  • Author: Emily
  • Total Time: 1 hour 38 minutes
  • Yield: 18 1x
  • Diet: Gluten Free

Description

Soft, chewy and swirled with creamy cheesecake filling, these Gluten Free Pumpkin Cheesecake Cookies are the perfect fall treat. They are cozy, decadent and guaranteed to disappear quickly!


Ingredients

Scale
  • 2 ½ cups gluten free 1-1 baking flour
  • 1 cup granulated sugar
  • ½ cup light brown sugar
  • 1 can (15 oz) pure pumpkin puree
  • ⅓ cup butter, melted
  • 1 egg
  • 1 tbsp pumpkin pie spice
  • 2 tsp baking powder
  • 1 tsp baking soda
  • 1 tsp pure vanilla extract
  • ½ tsp salt

Cream cheese filling:

  • ¾ cup cream cheese, softened
  • ¼ cup granulated sugar
  • 1 tsp pure vanilla extract

Instructions

  1. In a large bowl add sugar, brown sugar, pumpkin puree and melted butter. Using a handheld mixer, mix on low speed for 1-2 minutes until ingredients are evenly combined.
  2. Add in the egg and vanilla extract and mix again, scrape down the sides of the bowl to make sure everything is evenly incorporated.
  3. In a separate bowl, add the flour, pumpkin pie spice, baking powder, baking soda, and salt. Whisk together.
  4. Add half of the dry ingredients into the wet mixture and mix on med-low until all combined. Then add in the rest of the dry ingredients until fully combined. The cookie dough will be soft.
  5. Cover with plastic wrap and place in the freezer for 1 hour.
  6. Add cream cheese to a small bowl, then add in the sugar and vanilla. Mix until combined.
  7. Place a piece of parchment paper on a baking sheet and using a ½ tbsp, take a heaping scoop of the cream cheese filling and place onto the parchment paper. You should be able to get 18 dollops. Cover with plastic wrap and place in freezer until the cookie dough is ready.
  8. Remove cookie dough and cream cheese filling from the freezer. Preheat the oven to 350 F and line 2 large cookie sheets with parchment paper.
  9. Using a cookie scoop, scoop 6 mounds onto prepared baking sheet, 2-2 ½ inches in diameter and 1 inch thick. Place a cream cheese dollop on the center of the cookie mound then cover with a small amount of cookie dough and spread around to mostly cover the cream cheese. It is alright for a little bit of the filling to show.
  10. Place in preheated oven and bake for 18-20 minutes. The centers should no longer look wet. Repeat until all the dough and filling is used. You should be able to get 18 large stuffed cookies.
  11. Wait 5 minutes before transferring to a wire rack to cool. Enjoy!

Notes

  • Use fresh or canned pumpkin puree not pumpkin pie filling.
  • Use room temperature cream cheese and egg so that they will incorporate easily.
  • The cream cheese and cookie dough need to be placed in the freezer before baking.
  • Storage: Place any leftover cookies in an airtight container and refrigerate for 3-4 days. They must be refrigerated due to the cream cheese.
  • Freeze: Place cookies in a freezer bag or freezer friendly airtight container for up to 1 month.
  • Prep Time: 20 minutes
  • Cook Time: 18 minutes
  • Category: Dessert
  • Method: Baking
  • Cuisine: American

Nutrition

  • Serving Size: 18
  • Calories: 226
  • Sugar: 20.5g
  • Sodium: 173.3mg
  • Fat: 7.1g
  • Saturated Fat: 4.2g
  • Carbohydrates: 39.2g
  • Fiber: 1.3g
  • Protein: 2.4g
  • Cholesterol: 29.1mg

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