Mix the ricotta, spinach, egg yolks, grated cheese, nutmeg, salt and pepper together in a medium bowl until well combined. Stir in ½ cup flour until a sticky dough forms.
Pile the remaining cup of flour on a cutting board or plate. Drop a large spoonful of the dough (slightly larger than the size of a walnut) onto the flour and lightly toss it around in the flour until it is coated.
Gently form the dough into a ball with your hands, shaking off any excess flour. Repeat with the remaining dough. You should have about 24 gnudi in total. Discard the remaining flour or save for another use. Chill the gnudi in the fridge for 15 minutes while you make the sauce.
To make the sauce, heat the oil in a large skillet over medium heat. Add the onion and cook until softened, 7-8 minutes. Add the garlic and cook another 1-2 minutes, then stir in the tomatoes. Season the sauce with the oregano, salt, pepper, and sugar. Simmer the sauce for a few minutes and then stir in the basil.
Meanwhile, bring a large pot of salted water to a boil then lower the heat to a simmer. Working in batches, place the gnudi on a slotted spoon and gently lower them into the water. Cook the gnudi until they float to the surface of the water, about 4 minutes. Carefully remove them with a slotted spoon.
To serve, spoon some tomato sauce onto each plate and place the gnudi on top. Garnish with grated cheese.