Preheat the oven to 350 degrees F. Cover 2 sheet trays with parchment paper.
Whisk together the flour, cocoa powder, baking powder, baking soda and salt in a medium bowl.
Add the butter and sugars to a large bowl and beat with an electric hand mixer until light and fluffy, about 4 minutes. Add the vanilla and egg and beat until incorporated. Add the flour mixture in increments, beating until well combined. Briefly beat in the coconut flakes, chocolate chips and pecans until mixed together. Using your hands, roll the dough into walnut-size balls and drop 8 on a sheet tray, leaving 2 1/2 inches of space between them. Flatten them slightly. Bake 13 minutes. Let cool on the sheet tray 5 minutes.