Preheat oven to 350 degrees F. Line a large baking sheet with a silicone baking mat or parchment paper and set aside.
Make your flax egg by combining the ground flaxseed with water. Set aside for 5 minutes to thicken.
In a medium bowl, whisk together flour, baking powder, baking soda, and sea salt. Set aside.
Using a stand mixer, cream coconut oil and sugars together for about 3 minutes with the paddle attachment. I usually do it at a speed 4 in my Kitchen Aid. Add in the flax egg, vanilla, and almond milk and beat until combined.
With the mixer on low, slowly add in the dry ingredients. Add the chocolate chips, shredded coconut, and pecans and pulse the dough a couple of times until the mix-ins are fully incorporated. You can also stir by hand with a spatula if you want.
Form the cookie dough into balls, about 2 tablespoons of dough. Place on prepared baking sheet, about 2 inches apart.
Bake cookies for 10-12 minutes or until the edges are slightly golden brown. It will continue to cook and firm up as it cools. Remove from oven and let cookies cool on the baking sheet for 15 minutes. Sprinkle flaky sea salt on top. Transfer to a wire cooling rack and cool completely.
Enjoy! Store in an airtight container on the counter for up to 3 days.