Prep the pan: Heat oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
Mix dry ingredients: In a medium bowl, whisk flour, sugar, baking powder, baking soda, and salt.
Combine wet ingredients: In a large bowl, whisk eggs, buttermilk, oil, lime juice, lime zest, and vanilla until smooth.
Bring it together: Add dry ingredients to wet and whisk just until combined. Do not overmix.
Batter should be smooth with no dry pockets.
Fill and bake: Divide batter evenly among liners (about 2/3 full). Bake 16–19 minutes, until tops spring back and a toothpick comes out clean.
Cool completely: Let cupcakes cool in the pan 5 minutes, then transfer to a rack to cool fully before frosting.
Make the frosting: Beat cream cheese and butter on medium speed until creamy and fluffy, 2–3 minutes. Add powdered sugar 1 cup at a time, then mix in lime juice, zest, vanilla, and a pinch of salt.
Beat until smooth. Adjust sugar to reach a pipeable but creamy consistency.
Frost and garnish: Spread or pipe frosting on cooled cupcakes. Top with a sprinkle of zest or a tiny lime wedge.