Preheat oven to 350F. Line a mini muffin tin with mini paper liners. Set aside.
In a large bowl, mix the whole wheat flour, all-purpose flour, cocoa powder, baking powder, baking soda, salt, and flax seed. Set aside.
In a medium bowl, whisk the oil, milk, eggs, and vanilla. Add the white sugar, brown sugar, and zucchini. Mix to combine.
Add the wet oil mixture to the dry ingredients. Mix to combine.
Add the chocolate chips to the muffin batter. Mix to combine.
Measure about 1 heaped tablespoon into each mini muffin liner, until about 3/4 full. Bake for 15 minutes or until a wooden skewer inserted in the centre of a muffin comes out clean. Remove from oven and let cool 5 minutes in the tin before turning out muffins onto a wire rack to cool completely.
You can serve the muffins warm or cool.
You can also store the muffins for up to 6 months. Place them in a freezer bag, seal well, and store in the freezer.