Preheat the oven to 350 degrees F. Line two 12-cup muffin tins with paper liners.
Prepare the cake mix according to package directions. Fill the muffin cups with the batter. Bake according to package directions. Cool.
Using a melon baller, scoop out the center of each cupcake, scooping almost to the bottom of the cupcake. Spoon 1 generous teaspoon of applesauce into each hole. Frost the tops with cream cheese frosting. Sprinkle the cupcakes with chopped pecans.