For the crustPreheat oven to 425°F.
Combine the almond flour, tapioca flour, ground flax seeds, coconut sugar, salt, and coconut oil in a food processor, or use a pastry blender in a bowl. Pulse or blend until the texture of coarse meal, being careful not to over-blend the coconut oil.
Add the water and pulse or stir until the dough comes together. If you’re mixing in a bowl, you may want to use your hands to bring the dough together at the end.
Roll out the dough in between two sheets of parchment or on a silicone baking mat into a 12-inch circle. Carefully lay dough into a 9-inch pie dish (not deep dish). If the dough breaks, that’s okay! Just press it back into place and repair any holes/cracks that may have formed. Place in the freezer while preparing the filling.
For the fillingPlace the sliced apples in a large bowl. Melt the coconut oil or ghee in a saucepan over medium-low heat. Whisk in the tapioca flour to form a paste and then whisk in the coconut sugar, maple syrup, cinnamon, ginger, nutmeg, allspice, vanilla extract, and lemon juice. Bring to a boil and let simmer for 3 minutes before removing from heat and pouring the caramel sauce over the sliced apples. Toss to coat all of the apples, and pour into the prepared crust.
For the crumble topping, combine the almond flour, coconut flour, flaked coconut, maple syrup, coconut oil, and pecans in a mixing bowl. Stir until the dry ingredients are completely moistened and then crumble evenly over the apples.
Place the pie on a baking sheet and bake 15 minutes at 425°F. Reduce the temperature to 350°F, and continue baking for 35 to 45 minutes or until the apples are tender and the pie is golden brown on top. Tent with foil if the pie starts to brown too quickly!
Let cool for at least 1 hour, preferably 4 or more, before serving. Serve warm or chilled. Keep any leftovers stored in the refrigerator.