Preheat your air fryer to 400°F. Cut the spaghetti squash in half lengthwise, then scoop out the seeds. Season the insides of the squash generously with about 2 teaspoons of salt, ½ teaspoon black pepper, 1 teaspoon of Italian seasoning, and 2 tablespoons of olive oil. Air fry until soft and tender, about 15-20 minutes.
Meanwhile, in a skillet on the stovetop, heat the remaining olive oil, then add onion with a pinch of salt. Cook until softened, about 3-5 minutes, then add garlic, Italian seasoning, and red pepper flakes and cook until garlic is fragrant- about 30 seconds. Add the onion, garlic, and seasoning mixture to the ricotta, parmesan, and mozzarella and mix well.
Add the cheese mixture to the insides of the spaghetti squash and air fry for 3-5 minutes at 400°F until cheese is golden brown. Garnish with fresh herbs, salt, and pepper. Enjoy!
Store in an airtight container in the fridge for up to 3 days.