To prepare the spaghetti squash, preheat the oven to 400 degrees Fahrenheit and line a large, rimmed baking sheet with parchment paper for easy clean-up.
Use a very sharp chef’s knife to cut off the tip-top and very bottom ends of each spaghetti squash. Stand the squash upright on a stable surface and carefully slice through it from top to bottom to divide it in half. Repeat with the other squash.
Use a large spoon to scoop out the spaghetti squash seeds and discard them. Drizzle the insides of each squash half with 1 teaspoon olive oil and rub it all over the inside. Sprinkle salt and pepper lightly over the interiors of the squash, then place them cut-side down on the prepared baking sheet.
Bake for 40 to 60 minutes, until the cut sides are turning golden and the interiors are easily pierced through with a fork. Small squash will be done sooner than large squash, naturally! Leave the oven on for later.
Meanwhile, cook the spinach: In a large skillet over medium heat, warm 1 tablespoon olive oil. Add the garlic and sauté until fragrant, about 30 seconds to 1 minute. Add the spinach and cook, stirring often, until it’s wilted. Set aside.
Once the squash is done baking, fluff the interiors with a fork to make the insides spaghetti-like. Divide the spinach and Parmesan into the spaghetti squash and stir them into the squash. Season to taste with salt. Spread marinara sauce generously over each (feel free to eyeball this) and top with mozzarella.
Return the squash to the oven and bake for 20 minutes, or until the cheese is spotty brown. Sprinkle with fresh basil and red pepper flakes, if desired, and serve.
Storage suggestions: This recipe reheats well (I just warm them in the microwave). Leftovers keep well, covered and refrigerated, for about 4 days.
Change it up: You can cook leftover vegetables with the garlic, before adding the spinach. You could also use chopped kale, chard or collard greens instead of the spinach—those will just need a little more time in the skillet to soften.
*Parmesan note: Most Parmesans are not technically vegetarian (they contain animal rennet), but Whole Foods 365 and BelGioioso brands offer vegetarian Parmesan cheese.