Step 1

Preheat the oven to 400 degrees F (200 degrees C). Lightly grease a 9x13-inch baking dish with cooking spray.

Step 2

Combine yellow squash, zucchini, 1/2 of the Cheddar cheese, chile peppers, onion, and salt in a large bowl. Sprinkle with flour and toss to coat. Spread mixture into the prepared baking dish and cover with aluminum foil.

Step 3

Bake in the preheated oven until squash is tender and casserole is bubbly, 35 to 40 minutes. Remove from the oven and discard foil. Spread salsa on top and sprinkle with remaining cheese. Return to the oven and bake, uncovered, until golden and heated through, about 20 minutes more.

Step 4

Garnish with green onions just before serving.