Wash and dry all produce. Bring a large pot of salted water to a boil. Quarter zucchini lengthwise, then cut into 1/2-inch pieces. Halve, peel, and dice onions. Mince garlic. Strip thyme leaves from stems; discard stems. Roughly chop leaves.

Heat a large drizzle of olive oil in a large pan over medium-high heat. Add beef, breaking up meat into pieces. Cook, tossing, until browned but not yet cooked through, 4-5 minutes. Season with salt and pepper.

Add onions and zucchini to pan with beef. Cook, tossing, until softened, about 5 minutes. Add garlic, thyme, Italian seasoning, and soy sauce. Cook until fragrant, about 30 seconds.

Once water is boiling, add spaghetti to pot. Cook, stirring occasionally, until al dente, 9-11 minutes. Carefully scoop out and reserve 1 cup pasta cooking water, then drain.

Add crushed tomatoes and reserved pasta cooking water to pan. Bring to a boil, then reduce heat and let simmer until thick and saucy, about 5 minutes. Season with salt and pepper. TIP: If you have time, let the ragú simmer longer. It’ll just get better!

Add spaghetti to pan with ragú and toss to combine. Divide everything between plates, then sprinkle with Parmesan and chili flakes (to taste— you may want to leave them out for the little ones).