Preheat oven to 350 degrees. Spray a 9-inch square baking pan with Cooking Spray.
In a medium bowl, toss apple and pecans with 2 tablespoons flour to coat. In a large bowl, whisk together remaining flour, baking powder, nutmeg, and salt. In a small bowl, combine applesauce and yogurt.
In another large bowl, using an electric mixer, beat butter, granulated sugar, and orange zest on high until light and fluffy, 3 minutes, scraping down bowl as needed. Beat in eggs, one at a time, until combined. With mixer on low, add flour mixture in three additions, alternating with two additions applesauce mixture, and beat to combine. Fold in apple mixture. Transfer batter to pan and smooth top.
Bake until golden and a toothpick inserted in center comes out clean, about 50 minutes. Let cool in pan on a wire rack, 20 minutes. Using parchment, lift cake from pan. Dust with confectioners' sugar before serving.