Preheat the oven to 350°F (175°C) and line a heavy-duty baking sheet with parchment paper or a silicone baking mat.
In a medium mixing bowl, whisk together the sifted coconut flour, granulated sweetener, baking soda, and sea salt until no clumps remain.
In a separate small bowl, whisk the eggs and vanilla extract until well combined.
Add the melted butter and the egg mixture to the dry ingredients. Stir vigorously with a spatula until a uniform, thick dough forms.
Allow the dough to rest for 5 minutes; this is critical to allow the fiber-rich coconut flour to fully hydrate and absorb the moisture.
Gently fold in the sugar-free chocolate chips.
Using a 1-tablespoon cookie scoop, portion the dough into 12 equal balls and place them 2 inches apart on the prepared baking sheet.
Press down on each ball with the palm of your hand or a fork to flatten them to approximately 1/2-inch thickness, as coconut flour cookies do not spread during the baking process.
Bake for 10 to 12 minutes, or until the edges are just beginning to turn golden brown and the tops feel slightly firm to the touch.
Remove from the oven and allow the cookies to cool completely on the baking sheet for at least 15 minutes to firm up before handling.