Preheat your oven to 350°F, and lightly spray or line a muffin pan with parchment paper cups.
In a bowl, mix together the soy milk and apple cider vinegar to form a buttermilk mixture. Set aside.
Add all-purpose flour, cocoa powder, baking powder, baking soda, and salt to a large mixing bowl, and whisk or sift those together thoroughly until no clumps remain.
Add all of the remaining wet ingredients to the soy milk and apple cider vinegar, and stir together.
Pour the wet ingredients into the bowl of dry ingredients, and mix everything until just incorporated, making sure no flour patches remain.
Fold in the chocolate chips. Then, evenly divide your batter into the muffin pan, filling each cup about ¾ of the way full. Optional: sprinkle additional mini chocolate chips on top for decoration.
Bake the muffins for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the pan for 10-15 minutes before transferring them to a wire rack to cool completely (about 2-3 hours).
When the muffins have cooled, transfer them to an airtight container and store at room temperature for up to 3 days, or freeze for up to 3 months.