Preheat the oven to 350 degrees. Grease a 9 x 6-inch or 8x8 inch baking dish.
Peel and core apples then cut into thin slices. Transfer the apples to the baking dish. Add spices, lemon juice, agave syrup, butter, vanilla extract, and brown sugar on apples. Toss to combine.
Cover the baking dish with foil then bake in the oven for 35 minutes. Remove from the oven and remove foil. Stir with a wooden spoon, add the pecans and bake for an additional 25 - 30 minutes.