Preheat the oven to 350 degrees F. Line or spray a 12 cup muffin tin (could also use a 6 cup jumbo muffin tin).
In a large bowl, sift together the flour, sea salt, baking soda, cocoa powder, and powdered sugar. Set aside.
In a small bowl, whisk together the almond milk, applesauce, vanilla extract, and vinegar.
Making a well in the center of the dry ingredients, fold in the wet ingredients until just mixed together fully. Try and avoid over stirring. Gently stir 1/2 cup of the chocolate chips in.
Pour the batter evenly into the muffin tins, sprinkle with the remaining chocolate chips, and place in the oven. Bake for 15-18 minutes (assuming standard sized muffins). Muffins are done when a toothpick inserted into the middle comes out clean.