Prepare the Cream Cheese Pastry Crust: Pulse 1 1/4 cups flour and 1/8 teaspoon salt in a food processor until combined, about 3 or 4 times. Add 1/2 cup cold cubed butter and 4 ounces cold cubed cream cheese, and pulse until dough begins to clump together, about 10 to 12 times. Remove dough from processor, and gently shape into a flat disk. Wrap in plastic wrap, and chill 2 hours or up to 2 days.
Preheat oven to 425°F. Place cream cheese pastry disk on a lightly floured piece of parchment paper; sprinkle dough with flour. Top with another sheet of parchment paper. Roll dough into a 13-inch circle. Remove and discard top sheet of parchment. Starting at 1 edge of dough, wrap dough around rolling pin, separating dough from bottom sheet of parchment as you roll. Discard bottom sheet of parchment. Place rolling pin wrapped with dough over a 9-inch (1 1/2-inch-deep) glass pie plate. Unroll dough, and gently press it into pie plate. Trim dough, leaving 1/2-inch overhang; fold edges under, and crimp. Prick bottom and sides 8 to 10 times with a fork. Freeze until firm, about 20 minutes. Line pastry crust with parchment paper, and fill with pie weights or dried beans.
Bake in preheated oven 14 minutes. Remove weights and parchment paper, and bake until crust has lost its raw dough sheen, 5 to 7 minutes. Transfer to a wire rack, and cool completely, about 30 minutes. Reduce oven temperature to 375°F.
Prepare the Streusel: Stir together 1 1/2 cups flour, 1/2 cup brown sugar, 1/4 cup granulated sugar, 1 teaspoon cinnamon, and 1/4 teaspoon salt in a large bowl. Using a pastry blender, cut 4 ounces cold cubed cream cheese and 1/4 cup cold cubed butter into flour mixture until mixture resembles peas; stir in pecans. Using your fingers, work pecans into crumb mixture, forming small clumps of streusel. Cover and chill 2 hours.
Meanwhile, prepare the Apple Filling: Peel and core apples; cut into 1/2-inch-thick wedges. Toss apple wedges with 1/2 cup granulated sugar in a large bowl. Arrange apple wedges in a single layer on 2 large parchment paper-lined rimmed baking sheets. Bake in preheated oven until just tender, 20 to 25 minutes, switching pans top rack to bottom rack after 10 minutes. Remove from oven, and cool completely, about 15 minutes.
Melt 1/4 cup butter in a small saucepan over medium. Whisk in 3 tablespoons flour, and cook, whisking constantly, 1 minute. Add pepper jelly, 1/2 cup brown sugar, and 1/2 teaspoon cinnamon, and cook, whisking constantly, until sugar and jelly are melted and mixture is smooth, about 1 to 2 minutes. Remove from heat, and toss with roasted apple wedges in a large bowl.
Spoon apple mixture into prepared crust, packing tightly and mounding slightly in center. Sprinkle streusel over apples, and gently press. (It will seem like a lot of streusel, but the streusel will compact considerably as the pie bakes.) Place pie on a rimmed baking sheet.
Bake at 375°F on bottom rack until juices are bubbling, 45 to 50 minutes, shielding with aluminum foil after 25 minutes to prevent excessive browning, if necessary. Transfer to a wire rack, and cool completely, about 3 hours.
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