Heat your oven to 400 degrees F. Spray an 8-inch x 8-inch baking dish with non-stick cooking spray. Set aside.
In a large non-stick skillet, melt 1/4 cup unsalted butter over medium heat. Add the onion and cook for 6 minutes, until softened and translucent. Add the garlic and saute for 1 minute until fragrant.
Add in the zucchini and sprinkle it with salt, pepper, nutmeg, and flour. Mix and cook for 1 minute. Add in warm milk and stir until the mixture begins to thicken, about 1-2 minutes.
Take the skillet off the heat and stir in 1/2 cup of cheddar cheese.
Pour the mixture into the prepared baking dish and spread evenly. Top with the remaining cheese and crushed crackers. Drizzle with melted butter.
Bake for 18-20 minutes until the topping is golden brown and the zucchini is tender.
Remove from oven and allow to cool at least 15 minutes before serving. (This will help the sauce thicken.)