Home » cookies » Keto Salted Caramel (!!) Thumbprint Cookies 🍯

Keto Salted Caramel (!!) Thumbprint Cookies 🍯

Easy-peasy yet absolutely explosive! These gluten free and keto thumbprint cookies with a salted caramel filling will surely impress!

Gluten free & keto salted caramel thumbprint cookies with flakey sea salt
Gluten Free & Keto Salted Caramel Thumbprint Cookies

Keto Salted Caramel Thumbprint Cookies

Keto Salted Caramel Thumbprint Cookies

I dunno guys, I’m fairly certain our 15-minute (salted!) caramel has easily become my favorite fat bomb as of late. By the spoonful, in caramel lattes (!!), with Lily’s chocolate… and of course, with cookies!

And so these keto thumbprint cookies were sort of inspired by alfajores, the Argentinian sandwich cookies filled with dulce de leche (i.e. the South American caramel).

But this is definitely the lazy version! Because there’s no rolling, cutting out and fuzzing about the caramel getting everywhere. Fact is, they’re some of the least fussy (yet totally impressive!) cookies to whip up this Christmas!

A spoonful of sugar free and keto caramel sauce
Sugar Free, Low Carb & Keto Caramel Sauce

The Flours

To make these gluten free and keto, I cooked up a version of with almond flour and a touch of coconut flour.

And, just like in the snowball cookies, I’m going to suggest that you toast the almond flour beforehand. This is, in my book, the thing that takes this type of almond cookies to a whole other level. You’ll know what I mean the moment you mix the flours with the butter.

In terms of brands, for the almond either Anthony’s or WellBees work great. Both are super fine grinds. And for the coconut, I always favor Anthony’s (best taste by a mile!).

Freshly made keto thumbprint cookies with salted caramel filling
Gluten Free & Keto Salted Caramel Thumbprint Cookies

The Sweetener

The toasting of the almond flour gives such an intense flavor that most of aftertaste from keto sweeteners is masked (or at least greatly diminished!). So you’ve got a few options, just note that each sweetener will likely give you varying results in terms of texture. Think erythritol (a very slight cooling aftertaste, but best texture and no spreading… I like Lakanto’s monkfruit blend best), and xylitol or allulose (no aftertaste, but some potential spreading).

But the sweeteners must be powdered.

So get your blender out, make sure it’s completely dry, and process your sweetener of choice until powdered. Just make sure you wait a few moments for the dust to settle before opening the blender or food processor.

And if using xylitol, make sure to be careful if you have a pup around the house, as it’s highly toxic to the little guys! 🐕

Keto thumbprint cookies with a dripping salted caramel spoon
Gluten Free & Keto Salted Caramel Thumbprint Cookies
Keto salted caramel thumbprint cookies with a coffee
Gluten Free & Keto Salted Caramel Thumbprint Cookies

Gluten free & keto salted caramel thumbprint cookies with flakey sea salt

Gluten Free & Keto Salted Caramel Thumbprint Cookies

Easy-peasy yet absolutely explosive! These gluten free and keto thumbprint cookies with a salted caramel filling will surely impress!
Oh, and if baking with cups rather than grams is your thing, just click on US Cups for an instant conversion.
5 from 9 votes
Prep Time 20 minutes
Cook Time 15 minutes
Chilling Time 1 hour
Total Time 35 minutes
Course Cookies, Dessert
Cuisine American
Servings 20 cookies
Calories 103 kcal


For the filling


  • Add almond flour to a skillet or pan, and toast over medium heat until golden and fragrant (3-6 minutes). Remove from pan and set aside to cool completely (very important!). Whisk in the coconut flour, xanthan gum and salt, set aside. 
  • Cream butter in a large bowl with an electric mixer, 1 minutes. Add in sweetener and continue to beat until light and fluffy (7-8 minutes). Add in vanilla extract and egg, beating until just combined. 
  • With your mixer on low, add in half of your flour mixture- mixing until just incorporated. Mix in the rest. Wrap cookie dough with cling film (saran wrap) and refrigerate for at least an hour (and up to 3 days).
  • Preheat oven to 350°F/180°C and line a baking tray with parchment paper.
  • Divide dough into 20 rounds, press down to flatten and make an indentation with your thumb. Place shaped cookies on the prepared baking tray and place in the freezer for 15 minutes prior to baking.
  • Bake for 9-11 minutes. The cookies will be barely golden and still appear largely uncooked (worry not!). Transfer to a rack once they're manageable (they'll be very fragile for about 20 mins!). 
  • Make a batch of our salted caramel while the cookies are cooling. Transfer to a bowl and allow to come to room temperature. 
  • Spoon a dollop of caramel onto each cookie and allow to set. Depending on your room temp, you may need to pop them in the fridge so they set faster. Sprinkle with flakey sea salt right before serving!


*Please see section on Sweeteners for more deets on powdering and sweetening options.
The shaped dough can be frozen for up to 3 months, and they can be baked straight from the freezer (adding 2-3 minutes more to the baking time).
And if using xylitol, make sure to be careful if you have a pup around the house, as it’s highly toxic to the little guys! 


Serving: 1cookie | Calories: 103kcal | Carbohydrates: 2.5g | Protein: 1g | Fat: 10g | Saturated Fat: 3g | Cholesterol: 20mg | Sodium: 75mg | Potassium: 24mg | Fiber: 1g | Vitamin A: 155IU | Vitamin C: 0.1mg | Calcium: 13mg | Iron: 0.3mg
Keyword gluten free, grain free, keto, low carb, sugar free
Whip up this recipe?Comment below or drop me a line @gnomgnom._ and tag #gnomgnomyum!

Share the yummy-ness! 📷💨

If you made this recipe (or got a question!), be sure to simply comment below!

And do share your photo with your favorite Facebook group or tag @gnomgnom.yum on Instagram (I love seeing them all!!)

For The Holidaze!


  1. alina says:

    5 stars
    Gnom gnom is honestly the best keto community I’ve ever found! I read it all the time, and I’m also so grateful I found https://mmini.me/TheKetoWay. It helped me not only lead a much healthier lifestyle but also lose weight and keep it off. Hope it helps some others!

  2. Rebecca Valentine says:

    Wow. Looks amazing. Definitely trying this 😍
    Btw, I was wondering if you have a keto recipe for something like dark fantasy Choco fills. That is, chocolate cookies with liquid chocolate lava filling inside. If not, can you please consider this as my recipe request? *Pleads with puppy eyes* 😍🙈

  3. Anita Faulkner says:

    I don’t like caramel and would like to use Smuckers SF jelly. Should I put it in the indentation before or after baking?

  4. Danette says:

    Hi – I wanted to see if you have tried Sukrin. I started out with Swerve and then after trying the Lakanto felt that the cooling effect was much less that Swerve. Then I found Sukrin and find it to be even better…. just wondering if you have tried it and what your thoughts are about it.

    Made the Amaretti cookies and they are delicious – can’t wait to try these.

  5. Cat says:

    5 stars
    I love this recipe as written! The caramel filling makes them so rich and decadent. When I started my second batch I was a little brain dead and forgot to toast the almond flour. 🤦🏼‍♀️ Major blonde moment! Soooo, rather than risk the untoasted almond flour not working well with the caramel, I added a tablespoon of poppyseed, 1/2 tsp almond extract and filled them with your raspberry chia seed jam. OMG! Now I’m torn as to which version is my favorite. The almond/poppyseed/raspberry jam combo is awesome, summery and refreshing, but not as rich and decadent as the caramel. Jeez, guess I’ll just have to make both!

  6. Ola says:

    5 stars
    How can I substytute the xanthan gum? I would Love to made these😻
    PS your webstite is a blessing on keto! All recipes are amazing! Thank you 🙏🏻

    • Paola van der Hulst says:

      Awesome to hear Ola! You can use double the amount of flaxseed or just leave it out (they’ll be more fragile but not the end of the world) xo!

  7. Robyn Jacobs says:

    Could I add cocoa to the dough to make chocolate caramel thumbprints? How much would you recommend? Love that salted caramel sauce!!!!

  8. Sherry says:

    5 stars
    This was my last batch at the end of another long day of baking, after more than a week of baking all day every day, and I was out of steam. Rather than making the caramel, I filled the wells with ~1/4 tsp. Polaner sugar-free strawberry preserves with fiber; otherwise, everything else stayed the same. Absolutely delicious!

    We gift our neighbors with cookies every year and I’m going to try to sneak in another batch before Christmas. These are worth the effort!

    This is my first year of keto Christmas baking, and so far I’ve only had one recipe (not from gnom-gnom) that I wouldn’t add to the regular rotation. I’m using Lakanto monkfruit sweetener for most, since I dislike the cooling effect from some other sweeteners.

  9. Emily says:

    5 stars
    These are SO GOOD! That Caramel is beyond amazing I don’t know why it took me so long to finally make it! Between these beautiful thumbprints, the Biscoff cookies, and the fudgy brownies of yours I recently discovered, my family will be certain to love the cookie tins I’m sending this year! Thank you thank you thank you!

  10. Alissa says:

    So I know this question is a little out of the box, but I have loved all of your recipes and totally trust you to give it to me straight: With this being my first keto Christmas, I really miss almond thumbprint cookies. Do you think I could just substitute the 1 teaspoon vanilla with 1 teaspoon almond extract and call it a day? (I would plan to then use sugar free jam in place of the caramel.) Thanks so much in advance for your answer, but also thanks so much for testing and providing so many great recipes!

  11. Jennifer says:

    Can Swerve confectioners be used in place of grinding Erythirtol? The ingredients are erythirtol, oligosaccharides and natural flavors

      • Kate says:

        I agree about coconut flour – to me it just tastes dry and dusty. However, Ive only ever used Bobs Red Mill. I know you always recommend Anthony’s. Have you ever done a taste test comparison between the two? Thanks.

        • Paola says:

          Yeah there’s quite a difference in taste and texture between the two- it’s particularly noticeable in recipes like the tortillas which does rely more heavily in it. Here it’s only a couple tablespoons, and with all the flavors going on it’s only there to help with texture.

    • Paola says:

      Awesome to hear April!! Salted caramel ice cream is DEF on my to-do-list, and while I’m certain it’ll work I can’t give you an exact recipe (yet!!). What I’m thinking is that it could even just be folded into some whipped cream once cool… not sure yet if a pinch of xanthan gum is needed to stabilize it though xo!

      • Suzette says:

        Oh yes, a Salted Caramel Ice Cream would be phenomenal!! I know this is a super busy time of year but hopefully it’ll be happening sooner than later….please, please, pretty please!!! :))

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