Divide pie crust into 12 equal balls. Use your hands to flatten and stretch each ball into a round and place in a greased 12-cup muffin tin. Pat dough in the bottom and up the sides of cups. Place crusts in the fridge while you prepare the filling.
In a medium sauce pan over medium-high heat, melt butter then whisk in sugar and agave. Bring caramel to a simmer until golden-brown and thickened. Reduce heat to medium and stir in cream, spices, flour, and apples. Cook an additional 5 minutes until apples are slightly tender, then remove from heat and divide apple filling between crusts. Set aside.
Make the pecan topping: In a small bowl, whisk sugar, agave, butter, eggs, and vanilla until smooth. Fold in pecans and pour pecan topping evenly over apple filling.
Bake pies at 350F 25-30 minutes or until filling is bubbly, crust is golden, and the topping is set. (still slightly jiggly in the middle) Cool pies in pan 10 minutes then transfer to a wire cooling rack to cool completely. Enjoy!