Start by preheating your oven to 350°F (175°C) and lining a muffin tin with cupcake liners. A little trick: press the liners gently into the wells and add a tiny dab of butter or spray to make it easier to remove the cupcakes later.
In a mixing bowl, beat the softened butter together with the brown sugar until it’s light, fluffy, and creamy. Be sure to scrape down the sides of the bowl once or twice to catch any sugar that hides along the edges.
Add in the egg plus the extra yolk, milk, vanilla, and molasses. Mix gently until the batter comes together. If it looks a bit streaky or loose, that’s perfectly fine. Fold with a spatula from the bottom up to combine everything evenly without overmixing.
Now add the flour, baking powder, baking soda, salt, and all the warm spices, ginger, cinnamon, and nutmeg. Mix just until everything is incorporated; you want a smooth, spiced batter without overworking it.
Spoon the batter into the liners, stopping once they’re roughly two-thirds full. A cookie scoop works wonderfully to keep sizes even. Tap the pan lightly on the counter to level the tops for a smooth rise.
Bake for 19–20 minutes, or until a toothpick inserted in the center comes out with just a few moist crumbs. Set the cupcakes on a wire rack to cool until no warmth remains.
For the frosting, beat together the unsalted butter and cream cheese until fluffy and smooth. Add the powdered sugar, cinnamon, and a pinch of ginger, then mix until creamy. Finish with the vanilla for a cozy, spiced flavor.
Adjust the consistency by adding milk or a little orange juice one teaspoon at a time until the frosting spreads easily but holds its shape. Pipe or spread the frosting onto the cooled cupcakes, start from the center and swirl outward, or keep it rustic and fun. Top each one with a gingerbread cookie for a festive, playful touch.