Combine flour, sugar, and salt in a large bowl, then cut the cold butter cubes into the dry mixture using a pastry cutter, two knives, or your fingertips until the mixture resembles coarse breadcrumbs with pea-sized pieces of butter throughout. This texture is crucial for a flaky crust—the small butter pieces create steam pockets as they melt during baking. Don't overwork the dough or it will become tough. Set aside while you prepare the filling.
Peel and chop the zucchini into 1/2-inch pieces, removing any large seed centers. Add the zucchini and lemon juice to a large pot and bring to a simmer over medium heat. Cook for about 20 minutes, stirring occasionally, until the zucchini is very tender and begins to break down. Stir in the sugar, cinnamon, nutmeg, and cornstarch, then simmer for another 5 minutes to thicken the juices and meld the spices. I like to add the cornstarch near the end of cooking to prevent lumps and ensure the filling isn't runny when baked—this keeps the bars from becoming soggy.
Preheat your oven to 350°F. Press half of the crust dough evenly into a 9x13-inch baking sheet, working it up slightly along the sides to contain the filling. Bake for 10 minutes until the crust is set but not yet golden—this partial baking prevents a soggy bottom layer and helps the crust hold its structure under the wet filling.
Remove the partially baked crust from the oven and let it cool for just 1-2 minutes. Spread the zucchini filling evenly over the warm crust, then crumble or break the remaining crust dough into smaller pieces and distribute them over the top, pressing gently so they adhere slightly to the filling. Return to the oven and bake for 45-50 minutes until the top is golden brown and the filling bubbles slightly at the edges. The bars are done when the topping is set and firm to the touch.
Remove the bars from the oven and let them cool completely in the baking sheet on a wire rack—this usually takes 2-3 hours at room temperature. I find that cooling them fully helps them set properly and makes them easier to cut into clean squares without crumbling. Once cooled, cut into bars and store in an airtight container.