Preheat oven to 375 degrees F (190 degrees C). Line baking sheets with a silicone baking mats or parchment paper.
Whisk flour, cocoa powder, baking soda, and salt together in a bowl.
Beat butter, brown sugar, white sugar, eggs, and vanilla extract together in a bowl with an electric mixer until light and fluffy. Add flour mixture to butter mixture, 1/4 cup at a time, until dough is well-combined. Gently stir chocolate chunks, coconut, and pecans into dough. Scoop dough in 1-inch balls onto prepared baking sheets.
Bake in the preheated oven until cookies are set, 8 to 10 minutes. Cool completely.