Preheat oven to 400 degrees F. Set a wire rack on a rimmed baking sheet and set aside.
With a spoon, gently scoop out the gills that are inside the portobello mushrooms. Discard the gills and set the mushrooms aside.
In a medium bowl, add the ricotta cheese, egg, drained spinach, 1 cup of mozzarella cheese, ½ cup of the Parmesan cheese, lemon zest, basil, garlic powder, red pepper flakes, and pinch of nutmeg. Stir until well combined.
Divide the ricotta spinach filling between the Portobello mushrooms. Top each mushroom with ¼ cup marinara sauce and the additional mozzarella and Parmesan cheese. Season with salt and pepper, to taste.
Place the mushrooms on the wire rack and bake for 20-25 minutes or until the cheese is melted and mushrooms are tender. If you want to brown the cheese on the top, put the pan under the broiler for 1 minute. Make sure you watch the mushrooms closely, the cheese will brown quickly.
Remove from oven and garnish with basil. Serve warm.