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Step 1
Heat the oven to 425 degrees. Bring a large pot of salted water to a boil. Drain the tomatoes into a sieve or colander, lightly crush them with your hands and let them drain again while you prepare the dish.
Step 2
Meanwhile, heat 2 tablespoons of olive oil in a 10- or 12-inch, oven-safe skillet over medium heat. Add half the amount of the cauliflower, squash and shallot, season with salt and pepper and cook, undisturbed, until golden on the underside, about 4 minutes. Transfer the vegetables to a plate and repeat with 2 tablespoons olive oil and the remaining cauliflower, squash and shallot.
Step 3
Return all the vegetables to the skillet (it’s OK if things overlap at this point). Scatter the tomato pieces over the vegetables, then tear the mozzarella into pieces and arrange on top of the vegetables. Transfer the skillet to the oven and cook until the cheese is melted, the tomato juices are bubbling and the vegetables are fully tender, about 10 minutes.
Step 4
Meanwhile, add the spaghetti to the boiling water and cook according to package directions for al dente, usually 8 to 10 minutes.
Step 5
While pasta is cooking, heat the remaining 2 tablespoons of olive oil in a large skillet over medium heat. Add the garlic and chile flakes and cook, stirring occasionally, until the garlic is sizzling and golden, 2 to 3 minutes. Using tongs, drain and transfer spaghetti directly to the skillet with the garlic along with 1/2 cup pasta water. Increase heat to medium-high (any liquid in the skillet should be simmering vigorously) and cook, tossing, until liquid thickens and coats the pasta, about 2 minutes more. Remove from the heat and season with salt and pepper.
Step 6
To finish, heat the broiler. Broil the skillet of vegetables until the cheese is bubbling and golden in spots, 1 to 2 minutes. Serve vegetables alongside or on top of spaghetti.