a baking tray full of salted caramel chocolate thumbprint cookies

Low Carb Salted Caramel Chocolate Thumbprint Cookies

Chocolate and caramel collide in this grain-free, low carb Salted Caramel Chocolate Thumbprint Cookie. Rich, decadent, and moist these truffle-like cookies are the perfect vessel for a gooey, sugar-free salted caramel center.

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a hand holding a low carb salted caramel chocolate thumbprint cookie

Best Salted Caramel Chocolate Thumbprint Cookies – Low Carb, Keto, LCHF, Grain-free, Gluten-free, Sugar-free

Aside from chocolate and peanut butter, I would argue that there is only one other truly perfect dessert flavor combination out there:  chocolate and caramel. I will eat it in ice cream, pies, cakes, you name it. I love the two flavors separately, and I love them together. Buttery burnt sugar and rich cocoa are two elements that were naturally born to be paired together. I am totally prepared to enter into this dessert debate with you. I’m ready to admit that you might have some leverage if you bring up citrus based desserts, and possibly some valid points about how there are seasonal cycles of perfect desserts, but once you try these Salted Caramel Chocolate Thumbprint Cookies, you’ll see it my way. 

a baking tray lined with low carb salted caramel chocolate thumbprint cookies

As we start to prepare for the holiday season, I find myself seeking out desserts that fit into my ideal flavor archetypes in hopes of indulging in all my favorites during this time of the year. At Thanksgiving, I am still a firm believer in the power of pumpkin. These Pumpkin Cheesecake Bars are a perfect low carb way to celebrate with a pecan shortbread crust, fluffy spiced pumpkin cheesecake filling, and a vanilla creme fraiche topping. But as Christmas starts to ebb closer, I want indulgence and luxury. These Low Carb Chocolate Thumbprint Cookies are the perfect way to sneak in a sweet treat. These grain-free cookies travel well, and can easily be added to a cookie exchange or buffet table. If you are looking for something that might look a bit nicer on a dessert plate, consider my Salted Caramel Millionaire Bars or even my Citrus Almond Ricotta Cake. Any of these options will bring your guests back next year and will certainly wow your sugar-eating carboholic friends and family.

How to make Low Carb Chocolate Thumbprint Cookies


a baking tray with parchment and chocolate cookies

Some tips, tricks, and take-aways about the Grain-free Thumbprint Cookies with Caramel recipe and process:

Mix dry ingredients into the wet. Confession time:  I often just measure out and throw my dry ingredients into the wet without blending first. This is one recipe where you won’t want to do that because of how thick the batter is. After creaming the butter and erythritol, add the egg, melted chocolate, and extracts. You’ll incorporate the dry ingredients in a little at a time. Dough will be thick like a brownie cookie batter.

Roll dough ball before pressing your thumb in to create a divet. I find that you get a more uniform cookie if you roll your scooped cookie dough before placing it on the baking tray and using your thumb to create a crater for filling. It’s not an exact science, but they certain look a little less rustic.

Caramel is easy to make, unless you get it too hot. Caramel is not something you want to rush. Make sure that you keep the caramel on low as it cooks down otherwise it may split on you from the high heat. Also, once you pour it into a glass jar to cool down, let it cool down. I’ve rushed the process when the caramel was too thin and it runs out of the thumbprint and all over the cookie. I normally give my caramel at least an hour or two to cool and thicken up so it stays in bounds.

Other Low Carb Keto Cookie Recipes

Yield: 24

Salted Caramel Chocolate Thumbprint Cookies

Prep Time: 10 minutes
Cook Time: 30 minutes
Additional Time: 1 hour
Total Time: 1 hour 40 minutes

Chocolate and caramel collide in this grain-free, low carb Salted Caramel Chocolate Thumbprint Cookie. Rich, decadent, and moist these truffle-like cookies are the perfect vessel for a gooey, sugar-free salted caramel center.


Cookie Dough

  • 2 cups blanched, ground almond flour
  • 3 Tbsp coconut flour
  • 1/3 cup unsweetened cocoa powder
  • 1 tsp baking powder
  • 1/4 tsp xanthan gum
  • 1/4 tsp sea salt
  • 2 sticks salted butter, softened
  • 2/3 cup granular erythritol (Swerve)
  • 1 large egg
  • 2 ounces sugar-free dark chocolate, melted
  • 1 1/2 tsp pure vanilla extract
  • 1/2 tsp pure almond extract

Salted Caramel

  • 1 stick salted butter
  • 1/2 cup brown erythritol (Swerve)
  • 1/3 cup heavy cream
  • 1 tsp pure vanilla extract
  • 1/4-1/2 tsp sea salt
  • Flaked sea salt, if desired


  1. Preheat oven to 375 degrees. Line a baking tray with parchment paper. Set aside.
  2. In a medium bowl, whisk together flours, cocoa, baking powder, and salt. In a large bowl, cream butter and erythritol together until light and fluffy (about 3 minutes). Add egg, melted chocolate, and extracts. Blend to incorporate fully. Scrape down the sides of the bowl. Add half the dry ingredients. Mix to combine. Add remaining dry ingredients and mix until incorporated.
  3. Using a cookie scoop, scoop dough into 24 balls. Roll with your hands to even out. Set on your baking tray. Press your thumb in the middle of each cookie, about half way down, to create a well/divet for the caramel. Bake for about 10-12 minutes. Watch towards the end as chocolate cookies are not easy to discern color/burning. Remove from oven and cool completely.
  4. To make the caramel, melt the butter in a medium sauce pan over medium-low heat. Brown butter slightly, stirring frequently. Turn heat down to low. Add erythritol, heavy cream, vanilla, and sea salt. Stir to combine and dissolve sugar completely. Allow caramel to cook undisturbed on low heat for 15 minutes. Remove from heat and pour into a glass jar to cool. Caramel will thicken as it cools, at least one hour.
  5. Spoon caramel into the well/divet of each individual cookie. Top with flaked sea salt, if desired.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 154Total Fat: 15gSaturated Fat: 8gCholesterol: 42mgSodium: 141mgCarbohydrates: 3gNet Carbohydrates: 2gFiber: 1gSugar: 0gProtein: 2g

Nutrition is provided as a courtesy and calculated to the best of my ability using online databases. It is suggested that you perform your own check to ensure that a recipe fits within the scope of your dietary needs.

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