Preheat the oven to 400°F. Grease a 12-cup muffin pan with cooking spray.
Bring a large pot of salted water to a boil. Add the spaghetti and cook until al dente, about 10 minutes.
Drain the pasta, and then rinse it with cold water and add it to a large bowl.
Stir in 1 cup of the sauce until combined, and then stir in the shredded mozzarella cheese.
Using a large spoon and fork, twirl the pasta into nests and transfer it to the prepared muffin pan.
Top each cup with the remaining marinara sauce and mozzarella cheese.
Bake until the tops are golden brown and the edges are slightly crispy, about 15 minutes.
Remove the cupcakes from the oven and let them cool for 5 minutes. Using a spoon, transfer the cupcakes from the pan onto serving plates.
Garnish with Parmesan cheese and serve.
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