Preheat the oven to 350 degrees F. Spray 16 cups of mini muffin pans with nonstick spray.
For the crust: Beat together the cream cheese, brown sugar and butter in the bowl of a standing mixer fitted with a paddle attachment until light and fluffy, 1 to 2 minutes. Add the flours and salt and mix until the dough comes together. Break the dough off into 16 balls and press into and up sides of each muffin cup.
For the filling: Whisk together the pecans, brown sugar, butter, vanilla extract and egg in a large bowl. Fill each cup with 1 heaping teaspoon of filling. Bake until the crust is golden and the filling is set, about 17 minutes. Let cool completely before removing from the pans.