Place the onion in a large saucepan and sauté over medium heat for 10 minutes.
Add water 1 to 2 tablespoons at a time 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, vegetable stock, and orange zest and juice and bring the pot to a boil over high heat.
Reduce the heat to medium and cook, covered, for 25 minutes, or until the sweet potatoes are tender.
Puree the soup using an immersion blender or in batches in a blender with a tight fitting lid, covered with a towel. Return the soup to the pot and add the almond milk.
Cook for an additional 5 minutes, or until heated through, and season with salt and pepper.