In a bowl, whisk together the almond flour, coconut flour, baking soda, cinnamon, nutmeg and salt, and set aside.
Grab another bowl, and add the coconut sugar, coconut oil, almond butter, eggs, and vanilla extract.
Beat with a hand mixer or stand mixer.
Pour the dry ingredients into the wet ingredients, stirring until just incorporated.
Next, place the dough into the refrigerator for 30 minutes.
When the dough has been in the refrigerator for about 20 minutes, preheat the oven to 350 F, and line two cookie sheets with parchment paper.
Remove the dough from the oven, and form small cookie balls, and place them onto the cookie sheets.
Using the back of a spoon, press an indent into the center of each cookie.
Bake cookies 10-12 minutes or until lightly golden.
Remove from oven.
Use spoon to make the indent again, if needed.
Let cool completely.
Next, make the caramel sauce by adding the coconut sugar, coconut milk, and vanilla to a small saucepan. Bring to a boil over high heat, then reduce the heat to medium-low.
Simmer for about 30 minutes, stirring frequently, until the sauce reduces and thickens.
Transfer the sauce to a container to let cool.
When the caramel has cooled and thickened slightly (it will thicken the longer it sits), use a spoon to fill the center of each cookie with caramel.
Sprinkle with sea salt flakes, if desired (highly recommend)!