Prep your pan and oven. Heat the oven to 350°F (175°C).
Line a 12-cup muffin pan with paper liners. This recipe makes about 12–14 cupcakes.
Whisk the dry ingredients. In a large bowl, whisk flour, sugar, baking powder, baking soda, and salt until combined. This keeps the crumb light and even.
Combine the wet ingredients. In a separate bowl, whisk melted butter, eggs, buttermilk, lime juice, lime zest, and vanilla until smooth.
The mixture may look slightly curdled from the citrus—it’s fine.
Bring it together. Pour the wet mixture into the dry ingredients. Gently fold with a spatula until just combined. Do not overmix; a few small lumps are okay.
Fill the liners. Divide batter among the liners, filling each about two-thirds full. Overfilling can cause sunken centers.
Bake. Bake for 16–19 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
Rotate the pan once if your oven has hot spots.
Cool completely. Let cupcakes sit in the pan for 5 minutes, then move to a wire rack to cool fully before frosting.
Make the frosting. Beat cream cheese and butter on medium speed until smooth and fluffy, about 2–3 minutes. Add 3 cups powdered sugar, lime juice, zest, vanilla, and a pinch of salt. Beat until creamy.
Adjust with more powdered sugar for thickness or more lime juice for tang.
Frost and garnish. Spread or pipe the frosting on cooled cupcakes. Finish with lime zest, a tiny lime wedge, or a sprinkle of graham cracker crumbs for that pie feel.