Preheat oven to 375 degrees F.
Spray 9x13" baking dish with cooking spray and set aside.
In large skillet, heat olive oil over medium heat.
Add onions and bacon pieces and cook until onions are translucent and bacon is cooked, about 10-12 minutes.
In large bowl, combine sweet potatoes, apples, and onion/bacon mixture, including any grease from the bacon.
Add cinnamon, nutmeg, brown sugar, and salt and stir well to combine.
Pour into prepared baking dish.
Make pecan topping by combining melted butter, brown sugar, flour, salt, and diced pecans.
Sprinkle mixture over sweet potato mixture.
Bake in preheated oven for 50-60 minutes, until mixture is thoroughly cooked and golden brown.
Serve and enjoy!