In a large pot, cook the potatoes for 35 minutes in 4 cups of water.
Place the onion in a large saucepan and sauté over medium heat for 8 minutes. Add ¼ cup of the vegetable broth to keep the onion from sticking to the pan.
Add the garlic, ginger, thyme, nutmeg, and cinnamon and cook for 1 minute.
Add the sweet potatoes, the remaining vegetable broth, and miso. Bring to a boil over high heat.
Reduce heat and simmer, covered, for 35 minutes, stirring occasionally.
Add the almond milk. Cook for an additional 5 minutes, and season with a bit of pepper. Serve topped with a sprinkle of fresh thyme.