Preheat oven to 350 degrees F (175 degrees C). Grease an 8x8-inch baking dish and set aside.
Stir zucchini, apple, eggs, brown sugar, olive oil, and vanilla extract together in a bowl.
Sift whole wheat flour, all-purpose flour, cocoa powder, baking soda, kosher salt, and baking powder together in a separate bowl; gently stir into the zucchini and apple mixture until fully incorporated. Spoon batter into prepared baking dish. Sprinkle chocolate chunks and pepitas over the batter.
Bake in preheated oven until a tester comes out clean, about 25 minutes. Let cool before slicing.