Mix together the soy milk and apple cider vinegar in a medium-sized bowl.
In a small cup, mix together the ground flaxseed and water to make an "egg."
Set both aside for 15 minutes.
In a large bowl, whisk together the flour, sugar, cocoa powder and baking soda.
Mix the flaxseed mixture into the soy milk bowl, along with the butter, applesauce, and vanilla extract.
Pour the wet ingredients into the dry ingredient bowl and mix until all ingredients are incorporated. Fold in the chocolate chips. I leave some of the chocolate chips out to sprinkle a little on top after filling the muffin pan.
Fill the baking cups about 3/4 full with the muffin batter.
Bake for 18-20 minutes or until a toothpick comes out clean.