Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners.
In a medium bowl, sift (important) and whisk together the all-purpose flour and self-rising flour.
1 cup all-purpose flour, 3/4 cup self-rising flour
In a large bowl, beat the butter until smooth, about 2 minutes. Add the sugar and beat until blended. Beat in the eggs, one at a time. Add the lime juice, lime zest, and food coloring (if using). Mix until fully combined.
1/2 cup unsalted butter, 1-1/4 cups granulated sugar, 2 large eggs, 2-1/2 tbsps. fresh key lime juice , 1 tbsp. key lime zest, 1/4 tsp. neon green food coloring
Add the flour mixture in three additions, alternating with the buttermilk in two additions. Mix just until incorporated, don’t overmix, or the cupcakes won’t be light and airy.
3/4 cup buttermilk
Divide the batter evenly among the cupcake liners.
Bake until a toothpick inserted in the center comes out clean, about 18–22 minutes.
Remove the cupcakes from the pan and cool completely on a wire rack.
While the cupcakes cool, make the frosting. Beat the cream cheese, confectioners' sugar, butter, lime zest, and vanilla extract on medium speed until smooth.
1 (8 oz.) package full-fat cream cheese, 1-1/2 cups confectioners' sugar, 1/2 cup unsalted butter, 1 tbsp. plus more for garnish key lime zest, 1/2 tsp. vanilla extract
Pipe the frosting onto the cooled cupcakes. Sprinkle with extra lime zest, if desired.