Bring a large pot of salted water to a rolling boil. Add gnocchi and cook until they float, about 2-3 minutes. Drain and reserve ½ cup pasta water.

Heat olive oil in a large skillet over medium heat. Add diced onion and sauté until translucent and fragrant, about 5-7 minutes. Stir in minced garlic and cook for an additional minute.

Stir in pumpkin puree, heavy cream, and Parmesan cheese. Let simmer for about 5 minutes. Season with nutmeg, salt, and pepper to taste.

Fold in chopped spinach and cook until wilted, about 2-3 minutes. Incorporate the gnocchi into the sauce, using reserved pasta water to adjust consistency if needed.

Transfer to serving bowls and garnish with extra Parmesan, red pepper flakes, and fresh herbs if desired.