Prep the oven and squash: Preheat your oven to 400°F (200°C). Carefully slice the spaghetti squash in half lengthwise.
Scoop out the seeds with a spoon.
Season and roast: Spray the cut sides lightly with cooking spray and season with salt and pepper. Place cut-side down on a parchment-lined baking sheet. Roast for 35–45 minutes, or until the flesh is tender and easily shreds with a fork.
Start the sauce base: While the squash roasts, heat the olive oil in a large skillet over medium heat.
Add the diced onion with a pinch of salt and cook 3–4 minutes until softened. Stir in the garlic and cook 30 seconds until fragrant.
Add tomatoes and seasonings: Pour in crushed tomatoes, diced tomatoes, and tomato paste. Stir in oregano, basil, red pepper flakes (if using), and a small pinch of sugar or baking soda to reduce acidity.
Season with salt and pepper. Simmer uncovered on low for 15–20 minutes, stirring occasionally, until slightly thickened.
Cook the chicken: Pat the chicken dry and season with salt and pepper. You have two options: Skillet: Add a touch of oil to a separate skillet over medium heat.
Cook the chicken 5–6 minutes per side, until cooked through (165°F/74°C). Rest 5 minutes, then slice or dice.
Poach and shred: Simmer chicken gently in salted water for 12–15 minutes, then shred with forks. This keeps it lean and tender.
Add chicken to sauce: Stir the cooked chicken into the marinara and simmer 5 more minutes so flavors meld.
Taste and adjust salt, pepper, or herbs as needed.
Shred the squash: Remove squash from the oven and let cool a few minutes. Use a fork to scrape the flesh into long strands. Transfer to a bowl and season lightly with salt and pepper.
Assemble for meal prep: Divide the spaghetti squash among 4–5 meal-prep containers.
Top each with a generous portion of marinara chicken. Add fresh basil or parsley if you like. Finish with a sprinkle of Parmesan, if using.
Let it cool: Allow containers to cool with lids off for 10–15 minutes before sealing to avoid condensation.