Preheat an oven to 350 degrees F (175 degrees C). Grease 24 muffin cups, or line with paper muffin liners.
Prepare the filling by beating 1/4 cup sugar, cream cheese, 1 tablespoon lemon juice, and 1 teaspoon lemon zest with an electric mixer until smooth. Scoop the filling into a pastry bag, and set aside.
Whisk together the flour, baking powder, and salt in a mixing bowl; set aside.
Beat butter and 1 1/4 cups sugar with an electric mixer in a large bowl until light and fluffy. The mixture should be noticeably lighter in color.
Add the eggs one at a time, allowing each egg to blend into the butter mixture before adding the next. Beat in 1/4 cup lemon juice and 2 teaspoons lemon zest with the last egg. Beat in the flour mixture, mixing until just incorporated.
Pour the batter into prepared pans, filling the muffin cups half full. Pipe about 1 tablespoon of the filling onto the center of each cupcake, then top with the remaining batter to fill the muffin cup 3/4 full.
Bake in the preheated oven until the tops are light golden brown, about 15 minutes. Cook completely on a wire rack.
