Heat a pot over medium-low heat and add the bacon. Cook until it is crispy and the fat is rendered. Remove the bacon with a slotted spoon and place it on a paper towel to drain any excess grease.
With the pot still over medium heat, add in the onions and the garlic. Stir in the salt, pepper, paprika, cumin and nutmeg. Stir well to toss. Reduce the heat to low and cook until the onions become a bit caramely and golden, around 8 to 10 minutes.
Add in the pumpkin puree and stock. Stir and combine the mixture as much as you can. Turn off the heat and use an immersion blender or carefully transfer the soup to a blender to puree it until smooth. If you transfer it, put it back into the pot. Heat it over medium heat and bring it to a simmer. Let it simmer for 10 minutes or so.
After 10 minutes, stir in the cream. Taste and season the soup additionally with salt and pepper. Heat the soup until warmed through, then serve it topped with the bacon, chives and grilled cheese croutons.