Preheat your oven to 350°F (175°C) and lightly grease an 8x8-inch baking dish with coconut oil.
In a large mixing bowl, toss the sliced apples with lemon juice, 2 tablespoons of maple syrup, 1 teaspoon of cinnamon, and the nutmeg until the apples are evenly coated.
Transfer the apple mixture into the prepared baking dish, spreading them into an even layer.
In a separate medium bowl, combine the rolled oats, almond flour, chopped pecans, the remaining 1 teaspoon of cinnamon, and the sea salt.
Drizzle the melted coconut oil and the remaining 2 tablespoons of maple syrup over the oat mixture. Stir until the ingredients are well-incorporated and a crumbly texture forms.
Sprinkle the oat crumble evenly over the top of the apples in the baking dish.
Bake for 40 to 45 minutes, or until the apple filling is bubbling and the topping has turned a golden brown.
Remove from the oven and let the crisp rest for at least 10 minutes to allow the juices to thicken before serving warm.