Wash sweet potatoes and pierce each one a few times using a sharp knife. Place in a microwave oven and cook for 6 minutes.
Preheat the oven to 225 degrees F (110 degrees C).
Carefully remove sweet potatoes from the microwave oven and wrap each in aluminum foil. Place pecans on an oven-proof plate.
Place sweet potatoes in the back of the preheated oven and pecans in the front. Bake until pecans are toasted, 15 to 30 minutes.
Meanwhile, melt butter in a skillet over medium heat. Add apple, raisins, and cranberries and cook for 3 minutes. Stir in brown sugar, cinnamon, and nutmeg and cook 1 minute more. Remove from heat.
Remove sweet potatoes from oven and let sit for 15 to 20 minutes. Leave oven on.
Cut sweet potatoes in half lengthwise, scoop pulp into a large bowl, and mash using a potato masher. Add apple mixture and stir until blended. Spoon mixture into sweet potato shells and top with pecans. Place onto a baking sheet.
Bake in the hot oven for 20 to 30 minutes.
For lower sugar, use 1/4 cup sugar-free maple syrup.
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