Preheat the oven to 350°F. Lightly grease a 9×13-inch baking dish.
Make the pecan crust: In a large bowl, stir together the flour, melted butter, finely chopped pecans, and granulated sugar until well combined.
Press the crust mixture firmly and evenly into the bottom of the prepared baking dish.
Bake for 20–25 minutes, or until the crust is lightly golden. Remove from the oven and cool completely before adding the next layer.
Make the lemon cream cheese layer: Beat the softened cream cheese, powdered sugar, and 2 tablespoons of fresh lemon juice with an electric mixer until smooth and creamy.
Spread the cream cheese mixture evenly over the completely cooled pecan crust.
Make the lemon pudding layer: In a clean bowl, whisk the milk and both packages of instant lemon pudding mix for about 2–3 minutes, or until the mixture thickens. Let it stand for a few minutes if needed to reach a spreadable consistency.
Carefully spread the lemon pudding evenly over the cream cheese layer.
Add the whipped topping: Spread the thawed whipped topping evenly over the pudding layer.
If desired, sprinkle finely chopped pecans over the top.
Cover and refrigerate for at least 1 hour before serving. For the cleanest, most defined slices, refrigerate several hours or overnight.
For firmer slices, the dessert can be frozen overnight when using frozen whipped topping. Allow it to sit in the refrigerator for a short time before slicing.