Preheat your oven to 350°F (175°C) and prepare your muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking powder, and salt.
In a large bowl, cream together the softened butter and granulated sugar until light and fluffy, about 2-3 minutes.
Add the eggs one at a time, mixing well after each addition. Stir in the vanilla extract, milk, lemon zest, and lemon juice until just combined.
In another bowl, beat the cream cheese, powdered sugar, and vanilla extract until smooth.
Spoon a tablespoon of muffin batter into each cup, add a tablespoon of cream cheese mixture, and top with another tablespoon of muffin batter. Swirl gently with a toothpick.
Bake for 18-20 minutes, checking for doneness with a toothpick.
Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.