Preheat oven to 350 degrees F (175 degrees C). Butter 2 mini loaf pans (4 1/2x2 3/4-inch).
Combine coconut flour, flaked coconut, lemon zest, baking soda, and salt together in a bowl. Mix in yogurt, eggs, and maple syrup to form a smooth batter. Stir in chocolate chips. Pour batter into prepared loaf pans.
Bake in preheated oven until tops spring back when lightly pressed, about 25 minutes. Cover with aluminum foil and bake for an additional 5 minutes.
Cool muffins in the pans for 10 minutes before removing aluminum foil and turning out on a wire rack to cool completely.