In a large bowl, whisk together the flour, baking soda, baking powder, cocoa, and salt.
In a smaller bowl, combine the chopped berries and sugar and mash them together.
Add the flaxmeal mixture, oil, vanilla, and nondairy milk to the mashed berries and mix well.
Add the wet mixture to the dry ingredients along with the chocolate chips and blueberries. Stir together until everything is just mixed and you don't see any streaks of dry flour. Don't overmix.
Divide the batter equally between 12 muffin tins.
Bake in a preheated 350-degree Fahrenheit for 15 minutes or until a toothpaste inserted in the center comes out clean.
Remove to a rack, cool for 10 minutes, and when the muffins have cooled enough to handle remove them from the muffin tin and continue cooling on the rack.