Preheat oven to 400 degrees F (200 degrees C). Grease 12 muffin cups or line with paper liners.
Whisk chocolate chips, brown sugar, flour, cocoa powder, baking soda, baking powder, and salt together in a bowl. Whisk soy milk, oil, applesauce, eggs, vinegar, and vanilla extract together in a separate bowl; stir into flour mixture until batter is just combined. Spoon batter into prepared muffin cups until each cup is 3/4-full.
Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, 20 to 25 minutes.