Toss the sweet potatoes with 3 tablespoons butter on a half sheet pan and arrange in a single layer. Sprinkle with the cinnamon, nutmeg, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Roast until tender and lightly browned, about 30 minutes.
Meanwhile, in a bowl, mix the granola, pecans, remaining tablespoon butter, and a pinch of salt. Sprinkle over the sweet potatoes and gently press on top. Continue baking until the topping is browned, about 10 minutes.