Preheat oven to 325º. Spread two muffin tins with cooking spray with flour, or line with paper muffin liners.
In a mixing bowl, whisk together flour, cocoa, baking soda, baking powder, and salt; set aside.
In a large mixing bowl, combine eggs, agave, zucchini, oil, and vanilla and mix well. Add dry ingredients to wet ingredients and mix just until blended.
Divide batter into 24 muffin cups and sprinkle tops with chocolate chips. Bake approximately 20 minutes.