Pull the stems off the mushrooms, chop them, and set them aside. Brush any dirt off the mushroom tops.
In a large pan, sauté the chopped onion in olive oil until translucent, then the garlic along with chopped mushroom stems and thyme.
Once the stems are soft, deglaze the pan with wine (red or white will each give a very different flavor, but whichever you prefer), and then add water.
Put the mushrooms in pan, tops down, and spoon a bit of the juice over them. Let them simmer in the liquid for about 5 minutes.
While they are simmering, toast the almonds in a dry pan. Grind the toasted almonds in a coffee grinder, blender or food processor. Mix the ground almonds in a small bowl with 1 pinch of salt, pepper and nutritional yeast. You can use pre-ground almonds for this, they just won't have quite as much flavor.
Take the mushrooms out of the pan, and add the spinach to the pan. Sprinkle with 1 pinch of salt, allowing the spinach to just wilt.
Take the pan off the heat, and stir in the almond mixture.
Fill the mushroom caps with the filling, then put in a single layer on a baking dish and bake in a preheated oven at about 350 degrees F for 15-20 minutes. The mushrooms should start to turn golden, and the stuffing will start to brown.