Preheat oven to 400F. Spray a square baking dish with coconut oil (I like Spectrum Naturals) and set aside.
Cut spaghetti squash in half lengthwise and remove seeds. Spray the insides of squash with coconut oil (or olive oil) and sprinkle with salt and pepper. Place squash face down on a baking sheet and bake for 40 - 50 minutes, until you can shred the squash easily with a fork. (alternatively, you could cook the squash in the microwave for 10 - 12 minutes.)
Once the spaghetti squash is done, using a fork, scrape the squash away from the skin, separating it into strands of spaghetti and transfer to a small bowl.
Combine the squash, onion flakes, Italian seasoning, red pepper flakes and Greek yogurt and mix well. Transfer the mixture to your prepared baking dish and top with cheese.
Bake in preheated oven for 20 minutes, until golden brown on top.
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