Set your oven to 425°F (218°C). Line a standard 12-count muffin tin with paper liners.
For the crumble: Fork-toss the flour, sugar, and lemon zest together. Pour in the melted butter and stir until it forms distinct, clumpy crumbs. Set aside.
For the cheesecake: Whip the softened cream cheese, sugar, vanilla, and lemon juice together until completely smooth. Transfer to a piping bag or a ziplock bag with the corner snipped.
In a large bowl, rub the sugar and lemon zest together with your fingertips until fragrant and yellow. Whisk in the flour, baking powder, and salt. In a separate bowl, whisk the melted butter, eggs, sour cream, milk, lemon juice, and vanilla. Fold the wet ingredients into the dry ingredients just until combined.
Fill each of the 12 muffin cups about 1/3 of the way up with batter. Pipe a dollop (about 2 teaspoons to 1 tablespoon) of the cream cheese filling right into the center of each. Top with the remaining muffin batter, completely burying the cheesecake core.
Press the shortbread crumble generously over the tops of the 12 muffins.
Bake at 425°F (218°C) for 5 minutes to activate the rapid rise.Without opening the oven door, immediately drop the temperature to 350°F (177°C).Bake for an additional 12 to 15 minutes.
