Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
Whisk together flour, baking powder, baking soda, and salt in a medium bowl. Set aside.
In a large bowl, beat softened butter and sugar for 2–3 minutes until light and fluffy.
Add eggs one at a time, mixing well. Stir in vanilla, lime zest, and milk until smooth.
Gradually mix in the dry ingredients until just combined—don’t overmix.
Gently fold in fresh blackberries with a spatula, keeping them whole.
Spoon batter into liners, filling each ⅔ full. Bake for 18–20 minutes, or until a toothpick comes out clean. Cool in the tin for 5 minutes, then transfer to a wire rack.
Beat cream cheese, powdered sugar, and lime juice until smooth and fluffy.
Once cooled, remove a small center from each cupcake. Fill with cream cheese mixture using a spoon or piping bag.
Top with buttercream or whipped cream. Garnish with a blackberry, lime zest, and a small lime slice.