Place the spaghetti squash, cut side down, in the pan and allow to brown (approximately 5 minutes).*Note - This step is optional, but the extra browning of the squash will add more flavor to the final soup.Remove and continue the same process with the second squash.
Carefully place the browned squash in a microwave-safe dish (cut side down) and cover with plastic wrap, poking a hole in the plastic wrap for steam to escape.
Microwave on high power until the squash becomes tender (approximately 5 minutes) and when strands appear when the interior of the squash is scraped with a fork.Remove the squash from the oven and set it aside to cool.
Meanwhile, in the same skillet over medium/high heat ,brown and crumble the Italian sausage (approximately 7-10 minutes).
Add the onion, zucchini, and garlic to the sausage. Cook, stirring occasionally until the sausage is no longer pink in the center.
When the spaghetti squash is cool enough to handle, scrape the strands of the squash into a large stockpot.
Add the sausage mixture, oregano, basil, tomatoes, red pepper flakes, salt, black pepper, and chicken stock. Stir well.
Bring the soup to a simmer and cook (partially covered) over low heat for 20-30 minutes, stirring occasionally.
Remove from the heat and add in the butter and the apple cider vinegar along with additional salt and pepper (if desired).
Ladle the soup into bowls to serve and top each serving with Parmesan cheese.
Notes
Spaghetti Squash Soup freezes very well. Place in a freezer-safe container and freeze for up to 3 months.Tools and equipment:large skillet, large stockpot with lid, microwave-safe large bowl, plastic wrap, fork, measuring spoons, wooden spoons or spatula, ladle, can opener.