In a large mixing bowl, combine flour, sugars, and cheese, then add drained pineapple chunks along with nutmeg and cinnamon, stirring until thoroughly mixed.
Transfer the well-combined pineapple mixture into the greased baking dish, spreading it evenly across the surface.
Create the crumb topping by mixing cracker crumbs, melted butter, and reserved pineapple juice in a separate bowl until thoroughly combined.
Evenly spread the crumb mixture over the pineapple layer in the baking dish, ensuring a uniform topping.
Bake the assembled casserole in the preheated oven for 25-30 minutes until the edges turn a light golden brown.