Set the oven rack to the center position. Heat to 375ºF (191ºC).
Peel, core, and cut the apples into about 1/2-inch thick slices.
In a large bowl, stir to combine sliced apples, granulated sugar, brown sugar, flour (if using), cinnamon, nutmeg, salt, lemon zest, and lemon juice.
In a large skillet, melt the butter over medium heat. Add the apple mixture and saute until crisp-tender, and most of the moisture releases, about 15 to 20 minutes.
Lightly butter the bottom and sides of an 8 by 8-inch baking dish. Evenly spread the cooked apples inside.
In a medium bowl, whisk together the flour, brown sugar, granulated sugar, baking powder, cinnamon, and salt. Add the melted butter and vanilla. Stir with a spatula to combine and press together to make large clumps.
Evenly scatter the topping over the pre-cooked apples. Break them into dime-sized pieces along with some smaller ones.
Place the baking dish on a sheet pan. Bake until the topping is golden brown and crisp, about 30 to 35 minutes. Cool on a wire rack for about 30 to 45 minutes. This allows the topping to become crispier and for filling to set.
Serve warm with vanilla ice cream or whipped cream if desired.
Apple Substitutes: Golden Delicious, Fuji, Braeburn, Gala, or McIntosh apples taste similar to Honeycrisp. Use Granny Smith apples for more tartness.
Stronger Spiced Filling: Increase the cinnamon to 1 teaspoon, nutmeg to 1/2 teaspoon, and salt to 1/4 teaspoon.
Make-Ahead: The crumble topping can be refrigerated for up to 7 days or frozen for up to 1 month.
Make it in a Skillet: Bake inside an 8 to 10-inch cast iron pan.
Make it Gluten-Free: Substitute with gluten-free flour.
Make it Dairy-Free: Substitute coconut oil instead of butter.
Storing: Cool completely, then cover with foil or transfer to an airtight container. Refrigerate for up to 2 days.
Reheating: Heat individual portions in the microwave in 15 to 30-second intervals until warm. You can bake the whole dish at 350ºF (177ºC) until the top is crisp and the filling is warm.