Mix the ingredients for the crumble first and store in the refrigerator once combined. Use a fork or pastry cutter to cut in the cold/firm ghee or butter into the almond flour so it resembles coarse sand.
Shred the butternut squash and apples. Combine with remaining ingredients for the filling.
Pour the apple-butternut filling into a baking dish, then top with the cold crumble topping.
Bake for 35 to 40 minutes, or until the filling is bubbling and the crumble is golden brown.