Place spiralized zucchini (zoodles) into a pot and cover with well salted water; bring to a boil. Boil for 3 to 4 minutes, then empty into a colander to drain. Let drain for 2 to 3 hours, occasionally pressing out as much moisture as you can.
Preheat the oven to 375 degrees F (190 degrees C). Lightly spray a 9x13-inch glass casserole with cooking spray and add drained zoodles.
Bake zoodles in the preheated oven for 10 minutes.
Meanwhile, melt butter in a skillet over medium heat. Add onion and cook until soft and translucent, about 5 minutes. Add garlic and cook until softened, about 1 minute. Add cream cheese and cook until softened, about 2 minutes.
Remove zoodles from the oven and pour off any liquid. Add the skillet mixture to the zoodles, along with tuna, peas, Cheddar cheese, salt, and pepper. Stir until well combined. Sprinkle almonds on top.
Bake until cheese is melted and bubbly, about 30 minutes.