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Heat the oven and prepare the sweet potatoes. Arrange a rack in the middle of the oven, remove any racks above that rack, and heat the oven to 350°F. Scrub 3 pounds sweet potatoes and pierce all over with a knife.
Bake the sweet potatoes. Place the potatoes directly on the oven rack (place a sheet of aluminum foil onto a lower rack if you’re worried about drips). Bake until tender, about 1 hour. (Alternatively, microwave the sweet potatoes at 100% power for 12 to 15 minutes. Use tongs to flip halfway through cooking.)
Scoop out the flesh. Remove the potatoes from the oven and let cool until you can comfortably handle them, about 30 minutes. Halve each sweet potatoes lengthwise, then scoop the flesh out into a bowl; discard the peels. At this point, you can refrigerate the sweet potato flesh up to 3 days before proceeding; let come to room temperature before proceeding.
Prepare the pecan topping. Place 4 tablespoons unsalted butter in a medium microwave-safe bowl. Microwave at 100% power until melted, 20 to 40 seconds. Add 1 cup chopped pecans and toss to coat. Add 1/4 cup packed light brown sugar, 2 tablespoons all-purpose flour, and 1/8 teaspoon kosher salt, and toss with a fork to combine.
Prepare the baking dish. Coat a 2-quart soufflé dish or 8-inch square, 2-inch high baking dish with butter.
Make the soufflé base. Place 4 large eggs, 1/2 cup half-and-half or whole milk, 1/2 cup packed light brown sugar, 1 1/2 teaspoons kosher salt, 1 teaspoon ground cinnamon, and 1/2 teaspoon ground nutmeg in a food processor fitted with the blade attachment or blender. Process or blend until smooth and the sugar is mostly dissolved, about 30 seconds.
Blend in the sweet potatoes. Add the sweet potato flesh and process or blend until very smooth, about 30 seconds.
Add the flour and baking powder. Add 1/2 cup all-purpose flour and 1 teaspoon baking powder and process or blend just until combined, about 10 seconds. Do not overmix.
Transfer to baking dish and top with pecan topping. Transfer to the prepared baking dish and spread into an even layer. Sprinkle evenly with the pecan topping.
Bake 45 to 55 minutes. Bake until puffed and just set in the middle, 45 to 55 minutes. Let cool for about 5 minutes before serving.