Preheat the oven to 350 degrees. Grease a 9×13 baking dish. Toss the apples with the almond flour and cinnamon and spread across the bottom of the baking dish.
Whisk the coconut oil and honey together until smooth. In a large bowl, combine the rolled oats, pecans, almond flour, all spice, and salt. Add the coconut oil and honey mixture and stir until combined.
Pour the oat mixture over the apples to cover them evenly. Bake for 45 minutes until the topping is browning slightly. Let stand for 15-20 minutes to thicken before serving.