Preheat oven to 350 degrees F.
Line a 9" x 9" baking dish with parchment paper so that it hangs over the edges by about 1". Spray with nonstick cooking spray and set aside.
In a medium-sized mixing bowl, combine the graham cracker crumbs, flour, sugar, and salt and whisk together. Add the room temperature butter and mix with a pastry cutter (or your fingers) until the mixture is combined and slightly crumbly. Pat the graham cracker shortbread dough into the bottom of the prepared baking dish.
Bake in a preheated oven for about 8 minutes, or until lightly golden brown. Remove from the oven and cool for a minute before adding the cream cheese layer.
While the crust is baking, add the room temperature cream cheese and sugar to a large mixing bowl. Beat together using a handheld mixer until light and fluffy, or about 3 minutes. Add the egg and vanilla, then mix again on low speed until smooth.
Spoon the cream cheese mixture over the warm crust and spread even using an offset spatula.
In a large bowl, combine the lemon juice, lemon zest, sugar, and eggs. Whisk to combine, then add the flour. Whisk again gently, making sure it's combined and there are no lumps.
Pour the lemon filling over the cream cheese layer and place back in the oven for 35-40 minutes, or until the lemon custard is set and the edges are slightly golden brown. (Note: the cream cheese layer will rise to the top)
Once baked, remove the lemon bars from the oven and allow to cool completely at room temperature. Once cooled, transfer to the fridge for at least 1 hour before cutting into bars or squares.
To serve, pull from the fridge and dust with powdered sugar. They are best served chilled. Enjoy!