Preheat and prep the squash: Heat your oven to 400°F (200°C). Slice the spaghetti squash in half lengthwise and scoop out the seeds.
Drizzle the cut sides with 1 tablespoon olive oil and season with salt and pepper.
Roast the squash: Place the squash halves cut-side down on a parchment-lined baking sheet. Roast for 35–45 minutes, until the flesh is tender and strands easily pull away with a fork. Set aside to cool slightly.
Mix the meatballs: In a bowl, combine ground turkey, breadcrumbs, Parmesan, egg, grated onion, garlic, Italian seasoning, red pepper flakes (if using), 1/2 teaspoon salt, and a few grinds of pepper.
Use clean hands or a fork to mix gently until just combined. Do not overwork.
Shape the meatballs: Roll into 16–20 meatballs, about 1 1/4 inches each. Place on a plate or tray.
Cook the meatballs (stovetop option): Heat 1 tablespoon olive oil in a large skillet over medium heat.
Add the meatballs in a single layer and cook, turning occasionally, until browned on all sides, 6–8 minutes. Pour in the marinara, reduce to a gentle simmer, cover, and cook 8–10 minutes more, until the meatballs are cooked through (165°F/74°C).
Cook the meatballs (oven option): Alternatively, bake the meatballs on a lightly oiled, foil-lined sheet at 400°F (200°C) for 12–15 minutes, then transfer to a saucepan with marinara and simmer 5–7 minutes.
Shred the squash: Use a fork to scrape the spaghetti squash into strands. Toss with a pinch of salt and pepper.
If desired, stir in a teaspoon of olive oil or a spoonful of the marinara for flavor.
Serve: Divide the squash among bowls. Top with meatballs and sauce. Finish with fresh basil or parsley and extra Parmesan.