Preheat the oven to 400° and line a baking tray with parchament paper.
Cut the spaghetti squash in half lengthwise and remove the seeds with a spoon.
Brush the open faces of the squash with ½ tablespoon of olive oil and season with a pinch of salt and pepper.
Place the squash halves open face down on the parchament lined baking sheet and poke 4 holes into them.
Bake the squash for 35-45 minutes, until golden and easily peirced with a fork.
Once the squash is done baking, carefully fluff the insides to make spaghetti-like noodles. Remove as much of the noodles as you can without digging near the skin. Place them in a large bowl and set aside along with the emptied spaghetti squash halves. Leave the oven on.
Meanwhile, heat a large skillet over medium-high heat with the remaining ½ tablespoon of olive oil.
Once warmed, add the red onion, zuchinni, red pepper and cherry tomatoes. Cook for about 5 minutes, until the veggies begin to soften.
Add the garlic, dried herbs, a pinch of salt and pepper and chili flakes, if using. Cook for 2 minutes, until fragrant. Add the spinach and stir constantly until wilted.
Remove cooked veggies from the skillet and place them into the large bowl with the spaghetti squash noodles. Season with salt and pepper.
Pour ½ cup of the tomato sauce and 1 cup of the grated mozzarella into the bowl with the noodles and veggies. Stir until well combined.
Time to assemble the spaghetti squash pizza bowls. Divide the mixture of veggies, sauce and, cheese into each emptied squash half. Top with remaining tomato sauce and cheese.
Set oven to broil and bake until cheese is browned and bubbling. Be sure to keep an eye on it as it happens pretty quick, about 5-7 minutes.
Remove the squash bowls from the oven and let them cool. Top with parmesan and fresh basil, if desired. Serve immediately.