Preheat oven to 350ºF. Line a 12-cup muffin pan with cupcake liners and set aside.
In a medium bowl, add flour, baking powder, baking soda and salt; whisk and set aside.
In the bowl of a stand mixer, add sugar, butter and lime zest. Cream the ingredients for 3 minutes on medium speed using the paddle attachment.
Add one egg at a time, mixing well between each addition.
Add ½ dry ingredients, ½ milk and ½ lime juice; process on low speed before increasing to medium speed. Repeat with the remaining flour, milk and lime juice, cleaning the sides of the bowl.
Add vanilla extract and process until just blended.
Fill the prepared liners to 2/3rds full and gently tap the pan to dislodge any trapped air bubbles.
Transfer to the preheated oven and bake for 22 to 24 minutes or until a cake tester inserted in the center comes out clean with just a few crumbs.
While baking, combine Tequila and agave nectar; stir well and set aside
When done, remove the cupcakes from the heat and brush on with tequila-agave simple syrup. Allow to cool completely before frosting.