Preheat and Prepare: Preheat your oven to 350°F (180°C). Line a 12-cup muffin pan with cupcake liners or lightly grease the pan.
Mix the Dry Ingredients: In a large bowl, whisk together the flour, brown sugar, baking soda, cinnamon, salt, ginger, nutmeg, and cloves until well combined.
Combine the Wet Ingredients: In a medium bowl, whisk together the molasses, plant-based milk, oil, apple cider vinegar, and vanilla extract.
Make the Batter: Pour the wet ingredients into the dry ingredients. Stir until just combined—avoid overmixing to keep the cupcakes light and fluffy.
Bake the Cupcakes: Divide the batter evenly among the 12 cupcake liners. Bake for 20–25 minutes, or until a toothpick inserted into the center of a cupcake comes out clean. Let the cupcakes cool completely before frosting.
Make the Frosting: Using a stand mixer or hand mixer, beat together the vegan butter, shortening, powdered sugar, molasses, salt, vanilla extract, cinnamon, ginger, nutmeg, cloves, and plant-based milk until the mixture is light and fluffy.
Frost the Cupcakes: Once the cupcakes are completely cool, frost them generously with the salted caramel gingerbread frosting.