Wash the potatoes thoroughly under warm water then slice as thinly as possible. Preheat oven to 200°C.
Heat a small frying pan over medium heat with 2 tablespoons of the olive oil. Add the shallots and sauté for 10 minutes or until soft and translucent. Add the garlic and thyme and sauté a further two minutes.
Meanwhile, in a separate pan, heat the remaining olive oil on medium. Add the flour and stir to combine. Add the coconut milk and almond milk a little at a time, stirring in between to combine. Bring to a boil then add lemon zest, salt and nutritional yeast. Reduce heat to low and simmer for 10 minutes.
Add the onion and garlic to the milk mixture and stir through then season with black pepper to taste.
In a baking tray or casserole dish, layer half the potatoes then pour over half the sauce. Then repeat with remaining sauce and potato. Bake in prepared oven for 35 minutes. Serve immediately.