Preheat oven to 350°F (175°C) and line a baking sheet with parchment paper.
In a medium bowl, whisk together the all-purpose flour, cocoa powder, baking soda, and salt.
In a large mixing bowl, cream the softened vegan butter with granulated sugar and brown sugar until the texture is light and fluffy.
Incorporate the unsweetened applesauce and vanilla extract into the butter mixture, beating until well combined.
Gradually fold the dry ingredient mixture into the wet ingredients until no dry streaks remain.
Fold in the vegan chocolate chips using a spatula.
Scoop 1.5-tablespoon portions of dough onto the prepared baking sheet, maintaining 2 inches of spacing between each.
Bake for 10 minutes in the center of the oven.
Remove the tray and immediately press 3 to 4 mini marshmallows into the surface of each warm cookie.
Return the tray to the oven for an additional 2 minutes until marshmallows are slightly puffed.
Allow cookies to set on the baking sheet for 5 minutes before transferring to a wire cooling rack.