Preheat your oven to 350° F and lightly oil and flour a 12-muffin baking sheet. Mix the ground flax together with 3 tablespoons warm water and set it aside.
Whisk together the flour, baking powder, baking soda, salt, cocoa powder, sugar, and dark chocolate chips.
Whisk together the apple cider vinegar and non-dairy milk. Add the vegetable oil and applesauce, then stir in the flax mixture. Add the wet ingredients to the dry and mix until no more spots of flour are visible and the batter is mostly smooth (a few small clumps are fine). If the batter is stiff or very thick, add an extra 1-2 tablespoons non-dairy milk.
Scoop the batter into the muffin cups by the heaping 1/3 cup. Bake for 25 to 30 minutes, or until the muffins are firm on top. Cool completely before enjoying. The muffins will keep best when wrapped individually in plastic wrap and then stored in an airtight container.