Preheat the oven to 400°F. Line a baking sheet with parchment paper or a silicone baking mat.
Carefully remove the top of the squashes and scoop out the seeds. Season the inside flesh with salt and pepper; transfer the pumpkins to the prepared baking sheet and set aside.
In a medium skillet, add butter and sauté onions for 3-4 minutes or until softened. Add garlic and sauté with the onions for about 20 seconds, making sure not to burn.
Whisk in the flour and cook for about 2 minutes, stirring constantly, until the paste cooks and bubbles a bit, but don't let it brown. Slowly add the milk and cream, continuing to cook and stir as the sauce thickens. Squeeze as much liquid as possible from the spinach and add spinach to the sauce (feel free to add more milk or cream for a thinner sauce). Add nutmeg and lower the heat; cook, stirring for 2 to 3 minutes more. Add the Fontina, Gruyère, and ½ of the Parmesan cheese; mix well. Continue to cook for a few more minutes until the cheese starts to melt. Season to taste if needed, with salt and pepper. Pour the creamed spinach sauce into the pumpkin or pumpkins, reserve any extra creamed spinach if any, and bake in a ramekin. Sprinkle the remaining Parmesan all over, and close the pumpkin with the cap.
Bake the pumpkins (depending on the size and type of your pumpkin and your oven) for 45-55 minutes or until everything inside the pumpkin is bubbling and the flesh of the pumpkin is tender enough to be pierced easily with a fork or the tip of a knife. Remove the cap during the last 15 minutes of baking.
When the pumpkin is ready, very carefully (they are hot and wobbly) transfer to a serving platter. Serve with remaining warmed creamed spinach (if desired) and eat right away! Enjoy!