Preheat oven to 350 degrees and place liners in cupcake pan if using.
In a small bowl whisk boiling water into cocoa powder until smooth and combined. Set aside.
In another small bowl whisk together flax seeds and water and set aside to thicken.
Mix vinegar into almond milk and allow to sit a few minutes to make vegan buttermilk.
In a large bowl thoroughly combine flour, baking soda, baking powder, salt, and sugar.
After flax eggs haven thickened and milk has rested pour into dry ingredients, add applesauce and vanilla.
Stir just to combine and pour in chocolate mixture again stirring just to combine. Over stirring will make your cakes tough and dry.
Pour batter into pan wells filling ⅔ of the way and bake immediately for 15-18 minutes or until a toothpick inserted comes out clean.
Allow cupcakes to cool completely before frosting.