Pumpkin Cheesecake Keto Thumbprint Cookies

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The pumpkin spice season is bringing out the baker in me and this Pumpkin Cheesecake Keto Thumbprint Cookies Recipe is my second pumpkin-themed one for the blog!

To be honest, this is actually recipe #3, but the second recipe, also a cookie recipe was such an epic fail, the entire batch went in the trash.

It takes a lot for me to throw away a cookie, but when my cookie-loving husband couldn’t even tolerate them, I knew it was bad. I think it hurt his heart a little to admit there was such a thing as a bad cookie.

Why am I telling you this? Because I’m in no way an expert chef! But I do like to create food that is both yummy and satisfying. Food blogging includes many trials and errors, and at times, the wasting of many ingredients.

However! When a recipe comes together like these keto pumpkin cheesecake thumbprint cookies, I can’t wait to share them with the world!

Besides the yummy goodness of these cookies, they are also super easy to make! For the cookie dough part, you simply dump all the ingredients into the bowl at once, wet and dry alike.

Keto Thumbprint Cookies Ingredients

Then, simply beat with a hand mixer until all the ingredients are fully incorporated and form a nice dough.

Keto Thumbprint Cookies Mixing
Keto Thumbprint Cookies Mixed

Scoop cookie dough balls onto a parchment-paper-lined baking sheet using a 1-½ inch cookie scoop. Then, using your thumb, press a dent (or thumbprint) into the center of each cookie.

Keto Thumbprint Cookies Scooped Dough

Mix the filling ingredients in a medium bowl until smooth. Then spoon a dollop of the cream cheese filling into each of the cookie thumbprints.

Keto Thumbprint Cookies Cream Cheese Filling

Bake at 350 degrees F for 18-20 minutes, or until the cookie is browning and the cream cheese filling no longer jiggles.

Keto Pumpkin Cheesecake Thumbprint Cookies

Allow the cookies to cool for at least 20 minutes before transferring to a cooling rack to allow the cookies to fully set.

Store in the refrigerator for up to 1 week or freeze for later.

Be sure to check out my other pumpkin recipes too 🙂

Keto Pumpkin Pie Ice Cream

Keto Pumpkin Blender Pancakes

Watch the tutorial or scroll down for the printable recipe!

Now I have a favor to ask! If you enjoy this keto pumpkin cheesecake thumbprint cookie recipe, please give me a star rating in the recipe card below and share this post on your favorite social media platform ?

Keto Pumpkin Cheesecake Thumbprint Cookies

Pumpkin Cheesecake Keto Thumbprint Cookies Recipe

Yield: 26
Prep Time: 5 minutes
Cook Time: 20 minutes
Total Time: 25 minutes

If you haven't tried pumpkin cookies WITH cheesecake yet, stop what you're doing and make this recipe!


For the Cookies:

For the Filling:


  1. Preheat the oven to 350 degrees F.
  2. Combine all of cookie dough ingredients in a medium-sized bowl and mix together with an electric hand mixer until dough forms.
  3. Using a 1-1/2 inch cookie scoop, spoon the cookie dough onto a parchment-lined baking sheet.
  4. Use your thumb to dent the tops of each cookie with your thumbprint.
  5. Beat together the cream cheese, sweetener, egg, and vanilla in a medium bowl until smooth.
  6. Spoon the cream cheese filling into each cookie thumbprint.
  7. Bake the cookies for 18-20 minutes, or until golden brown and the tops no longer jiggle.
Nutrition Information:
Serving Size: 1 cookie
Amount Per Serving: Calories: 96.36Total Fat: 8.85gSaturated Fat: 2.96gSodium: 51.48mgCarbohydrates: 2.23gFiber: 1gSugar: 0.59gProtein: 2.74g

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    1. Hey MC! Since going keto, I always use salted butter to help keep my electrolytes up. But you could use either one. I don’t notice a flavor difference between the two.

  1. It’s unclear how much cream cheese is required. 13.4 ounces? Would love to make these – they sound delish!!

    1. Hey MJ. Sorry about the measurement confusion! My recipe plugin was glitching on me. It should be 4 ounces of cream cheese. I am getting this fixed now 🙂 And apparently I should check my other recipes too!

    1. Unfortunately not. Coconut flour and Almond flour do not convert evenly. Typically, you would use about 1/4 the amount of coconut flour but would need to significantly increase the liquid/wet ingredients. I haven’t figured out the exact conversion rate yet, lol…a bit of trial and error. I do want to start including more coconut flour in my baking though because I know many people have nut allergies.

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