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To make caramel: Combine all ingredients in a saucepan over medium heat. Once the mixture begins bubbling reduce heat and simmer for about 14 minutes, stirring frequently, until mixture is reduced and thickened. Pour into a jar and place in the fridge to cool (it will thicken when cooled).
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Preheat your oven to 350 F and line a large cookie sheet with parchment paper.
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In a large bowl, cream together coconut oil, sugar, honey, and egg until will combined. Stir in salt, vanilla, and baking soda. Add cassava flour and tapioca starch and stir until well combined.
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The dough should be moldable, otherwise add another tablespoon of flour to help thicken it.
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Roll about a tablespoon and a half of dough into a ball and place it on the baking sheet. Press down with your thumb to make an indentation in the middle and then repeat with the rest of the dough.
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Bake for 10 minutes, or until slightly golden on the edges. Place cookies on a cooling rack to cool completely. Once cooled, fill each thumbprint with a small spoonful of caramel. Top with sugar and sea salt if desired.