Finely chop the 1/2 onion, leeks and garlic. Heat a large pot over medium heat. Add 2 tsp of oil of choice.
Once warm, add the chopped onion. Stir, and then after a few minutes add the leeks and the garlic. While the onions and garlic are sauteing, wash and chop the potatoes and apple.
Once the onions are fragrant and golden, add the apple and potatoes. Stir to incorporate. Add salt and pepper, and chopped thyme. Let saute for 2-3 minutes, then add the vegetable broth.
Bring the soup to a boil, then simmer and cover for 18-23 minutes, until the potatoes are soft, but not mushy.
Transfer soup into a high-speed blender. Careful to not over blend the soup or the texture will become gooey from the potato starch. Start with a few pulses and then blend for 10 seconds (give or take). The soup should be smooth.
Transfer back to the pot and add the nutritional yeast. Heat on low for a few minutes, add more salt and pepper if desired. The soup stores in the fridge for 5 days.