Preheat the oven to 400°F (200°C) and line a baking sheet with parchment paper.
Slice the spaghetti squash in half lengthwise, remove the seeds with a spoon, and season the interior with salt and pepper.
Place the squash halves cut-side down on the baking sheet and roast for 40 to 45 minutes until the flesh is easily pierced with a fork.
In a large mixing bowl, combine the shredded chicken, Greek yogurt, blended cottage cheese, chopped spinach, artichokes, minced garlic, onion powder, and red pepper flakes.
Fold in 1/4 cup of the mozzarella cheese and 2 tablespoons of the Parmesan cheese into the protein mixture.
Remove the squash from the oven and use a fork to scrape the flesh into strands, ensuring the strands remain inside the squash skins.
Distribute the protein mixture evenly between the two squash halves, folding it gently into the squash strands to incorporate.
Top each half with the remaining mozzarella and Parmesan cheese.
Return the stuffed squash to the oven and bake for 10 minutes, then broil on high for 2 minutes until the cheese is golden and bubbling.
Serve immediately, ensuring each portion contains half of the total squash and filling to meet the 45g protein target.