Preheat the oven to 375°F. Line 2 baking sheets with parchment paper.
In the bowl of a stand mixer fitted with the paddle attachment, add the butter, coconut sugar, and vanilla extract. Mix on low until combined and there are no butter chunks.
Add the coconut milk and dry ingredients: flour, baking soda, and sea salt in that order. Mix on low until combined.
Then add the chocolate chips and mix to combine.
Using your hands, or a cookie scoop, form the dough into 20 balls and place on each parchment-lined baking sheet, you'll have about 10 cookies per sheet. Flatten them so they are about 2-inches in diameter (these will not spread) so the size the cookie dough is will be the size of the cookie. If you want to add extra chocolate chips on top of each dough ball, now is the time!
Bake for 12 to 14 minutes, or until golden brown around the edges. Sprinkle with flaky sea salt immediately after they come out of the oven. Allow to cool completely on the baking sheet.
Store in an airtight container for up to 7 days.