Preheat the oven to 350 degrees F. Lightly coat a 9x13-inch baking dish with nonstick cooking spray.
Place the sweet potatoes in a large pot and cover with water. Bring to a boil and cook for 10 to 15 minutes, or until just fork-tender. Drain well.
Transfer the sweet potatoes to the prepared baking dish.
Add the apples and flour. Toss gently until evenly coated.
In a small mixing bowl, whisk together the melted butter, brown sugar, cinnamon, nutmeg, and salt.
Drizzle the butter mixture evenly over the sweet potato and apple mixture.
Bake for 30 minutes, or until the apples are tender and the casserole is lightly browned around the edges.
Remove from the oven and sprinkle with the chopped pecans.
Let the casserole rest for 5 minutes before serving.
Christina's Notes
Cut the sweet potatoes and apples into evenly sized pieces so they cook at the same rate.
Avoid overcooking the sweet potatoes during boiling. They will continue to soften while baking.
If your apples are especially sweet, reduce the brown sugar slightly.
For extra crunch, toast the pecans in a dry skillet before adding them to the casserole.
This casserole can be assembled up to 24 hours in advance and refrigerated before baking.
Store leftovers covered in the refrigerator for up to 4 days.
Reheat in a 325 degree F oven until warmed through.