In a small bowl, combine flour, cocoa and salt. Set aside. In a large bowl, cream the butter and sugar together until fluffy. Add the eggs, one at a time, whisking until smooth after each addition. Whisk in the vanilla. Slowly add the flour mixture to the wet ingredients and mix until combined. Do not overmix. Pour batter into prepared pan and spread evenly. Set aside.
In a bowl, with an electric mixer on medium speed, beat cream cheese, egg, sugar and vanilla until fully incorporated and smooth, scraping down the sides if necessary. Spread this cream cheese mixture evenly over the brownie layer. Set aside.
In a medium bowl, toss the apples with the pecans, cinnamon and nutmeg. Sprinkle this apple mixture evenly over the cream cheese layer and press gently so that they adhere.