stack of caramel thumbprint cookies

Deliciously rich and lush vegan salted caramel thumbprint cookies that are undetectably Paleo and gluten free! The perfect healthy and allergen friendly Christmas cookie!

These vegan salted caramel thumbprint cookies are a bit life changing, I’m not going to lie.

The Paleo thumbprint cookie base is undetectably gluten free, vegan, and dairy free, yet is perfectly chewy and soft with delicious hints of vanilla. Then of course, there’s the decadently lush Paleo vegan caramel sauce filling with just a sprinkle of flaked sea salt.

two vegan caramel thumbprint cookies stacked

Basically, these vegan thumbprint cookies are the epitome of both elegance and decadence, and you’re going to need to make these STAT for your next party or cookie exchange!

Especially since they’re very allergy friendly, meaning anyone can have one!

bitten paleo caramel thumbprint cookie with caramel spoon

What makes these caramel thumbprint cookies Paleo, vegan, and gluten free?

What I love about these Paleo vegan caramel thumbprint cookies is that you really cannot tell that they’re free from the top 8 allergens.

Instead of eggs, we’re using ground flaxseed or unsweetened applesauce, and instead of flour, we’re using cassava flour, which is a Paleo flour made from the cassava root.

stacks of vegan caramel cookies with sea salt on top

What’s more, we’re using coconut oil in lieu of butter and dairy free milk in place of regular.

And yet, these vegan caramel cookies somehow still taste like any other Christmas or holiday cookie you’ll make: absolutely decadent and irresistible! I blame it on the caramel 😉

bitten caramel thumbprint cookie

How to make vegan salted caramel thumbprint cookies

We’ve mentioned a few of the ingredients above, but I want to make sure you’re stocked up on what you need to make these caramel thumbprint cookies:

spoon in jar of paleo caramel sauce

Then we’ll basically make these cookies in three major steps: the caramel sauce, the actual cookie part and then the filling!

Before you begin with making the cookies, you’ll need to make the vegan caramel sauce. Follow the directions in the post, chilling the caramel sauce while you prepare the cookies.

To start, you’ll preheat the oven and make the dough (see recipe card below).

triple stack of vegan caramel thumbprint cookies

Then you’ll form the cookies into thumbprint cookie dough shape: rolling a ball of dough in your palms, placing the dough ball onto the baking sheet, and pressing your thumb into the middle of the cookie.

Do this for all of the cookies, then bake!

Once the vegan thumbprint cookies are baked and cooled, you’ll fill them with about 1 teaspoon of vegan caramel sauce.

Sprinkle with a little extra sea salt, and place them into the fridge to chill for 30 minutes so that they set!

caramel thumbprint cookies on board

Do you fill thumbprint cookies before or after baking?

Honestly, it depends on the filling! For these vegan caramel thumbprint cookies, you’ll fill them after, as baking would make the caramel too runny and create a mess.

However, if you’re filling them with a jam, you’ll fill them before. See the next section for some filling recommendations and baking suggestions!

caramel thumbprint cookies with sea salt

Can I fill these vegan thumbprint cookies with other fillings?

Absolutely! Of course, I highly recommend the caramel sauce, but if caramel isn’t your thing, then here are a few other options:

  • Bake some homemade strawberry jam in the middle of each cookie (fill the cookie dough with jam before you place it into the oven!)
  • After baking the cookies, quickly place a few chocolate chips into the middle of each cookie to let the chocolate melt
  • Fill with homemade peanut butter, homemade cashew butter, or even coconut butter!
wooden board with caramel thumbprint cookies stacked

Can you prep these thumbprint cookies ahead of time?

Absolutely! In fact, they’re best this way. I recommend making the caramel sauce the day before, but if you’re pressed for time, you can do it all in one day.

Actually, the caramel thumbprint cookies are best when they’ve set for a while, so making the day before is recommended if you can! However, if you need to fill them right before the holiday party, just make sure you give the cookies 30 minutes to set in the fridge 🙂

single bitten vegan caramel cookie

I hope you love these vegan salted caramel thumbprint cookies as much as I do! If you make them, let me know down below in the comments section.

As always, I love to see your beautiful creations on Instagram and Pinterest, so be sure to tag me there.

Happy Thumbprint Cookie making!

stacked caramel thumbprint cookies

More vegan Christmas cookies

Paleo Vegan Sugar Cookie Cut outs

Paleo Vegan Linzer Cookies

Vegan Gluten Free Gingerbread Cookies

Paleo Vegan Chocolate Chip Almond Butter Cookie Cups

Double Chocolate Chip Cookies

Paleo Vegan Slice n’ Bake Cookies

Healthier Ginger Molasses Cookies

Vegan Meringue Cookies

Vegan Gingerbread House

Want to save this recipe for later? Add it to your favorite recipe board on Pinterest!

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stack of caramel thumbprint cookies

Vegan Salted Caramel Thumbprint Cookies (Paleo)

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  • Author: thebananadiaries
  • Prep Time: 10
  • Cook Time: 13
  • Total Time: 23 minutes
  • Yield: 24 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American
  • Diet: Vegan


Deliciously rich and lush vegan salted caramel thumbprint cookies that are undetectably Paleo and gluten free! The perfect healthy and allergen friendly Christmas cookie!


  • 1 1/2 cup cassava flour (or 2 cups regular flour or gluten free 1-to-1 baking flour)
  • 1/2 cup coconut oil or vegan butter, softened but still cold
  • 1/2 cup coconut sugar
  • 3 tbsp ground flaxseed with 7 tbsp water or 1/3 cup unsweetened applesauce
  • 2 tsp vanilla extract
  • 1/2 tsp baking soda
  • 1/2 tsp sea salt
  • 23 tbsp dairy-free milk (optional)
  • 1 batch vegan salted caramel sauce
  • Flaked sea salt for garnish


  1. Prepare the vegan caramel sauce before making the recipe.
  2. If using a flaxseed “egg” instead of applesauce, prepare the flaxseed “egg” now by whisking 
  3. Preheat the oven to 350F and line a baking sheet with parchment paper.
  4. In a medium bowl, beat together the coconut oil, coconut sugar, ground flaxseed mixture or applesauce, and vanilla extract until combined. 
  5. Sift in the cassava flour, baking soda, and sea salt, and fold the flour into the wet ingredients. If the mixture isn’t combining enough, you can add in the dairy-free milk, starting with 1 tbsp and working your way up if you need more.
  6. Use a small cookie scoop to scoop a ball of dough, roll it in your palm, and then lightly press your thumb into the middle of the dough ball and forming the bottom of the cookie flat to sit onto the baking sheet. Place the cookie dough ball onto the baking sheet and fix any cracks if any. Repeat for the remaining dough. You should get between 20-24 cookies.
  7. Place the cookie sheet into oven and bake for 11-13 minutes, or until the cookies look set and have a light golden color to them.
  8. Remove from the oven and let cool for 20 minutes.
  9. After cooling, spoon about 1 tsp of caramel sauce into the middle of each caramel thumbprint cookie and top with flaked sea salt.
  10. Store in an airtight container for up to 2 weeks in the fridge or up to a month in the freezer.


  • Serving Size: 1 cookie
  • Calories: 111
  • Sugar: 7.5 g
  • Sodium: 110.4 mg
  • Fat: 6.1 g
  • Saturated Fat: 4.6 g
  • Carbohydrates: 13.5 g
  • Fiber: 0.7 g
  • Protein: 0.5 g
  • Cholesterol: 0 mg
pinterest image for salted caramel vegan thumbprint cookies
pinterest image for salted caramel vegan thumbprint cookies