Preheat the oven to 350°F. Line a 12-cup and 6-cup muffin tins with paper liners.
In a large bowl, sift the flour, sugar, cocoa powder, baking powder, salt and baking soda together, whisking to blend.
In a medium bowl, whisk together the plant-based milk, coffee, oil, vinegar and vanilla extract. Add this to the flour mixture and whisk just until combined. Do not overmix.
Fill the paper liners about 2/3 full with the cupcake batter. Bake for 20-22 minutes or until a toothpick inserted comes out clean or with a few cooked crumbs. Cool the bases in the tray for 5-10 minutes and then transfer each cupcake to a cooling rack. Let cupcakes cool completely before frosting.