Preheat the oven to 350 F and line a baking sheet with lightly-greased parchment paper.
Add the almond butter, coconut sugar, maple syrup, coconut oil, and vanilla extract to a bowl and cream together until fully combined.
Combine the almond flour, arrowroot, and baking powder in a separate bowl. Add the dry ingredients to the wet and stir to combine until a dough forms.
Use a small cookie scoop (or your hands) to roll small cookie dough balls. You'll have about 16-18. Add to the baking sheet and slightly flatten. Use your thumb to press an indent into the cookies.
Bake the in the preheated oven for 15-17 minutes or until the cookies are golden brown. Remove from the oven.
While the cookies are still warm (but not hot), carefully add about 2-3 chocolate gems to the center of the cookies. The heat will melt the chocolate. (see notes)
Serve the cookies while the chocolate is still slightly melted (but not hot) or allow to chill before serving.