Preheat the oven to 350 degrees.
Combine the almond flour and almond milk in a bowl, and allow to sit for 5 minutes.
Knead together the ground beef, egg, onion soup mix, Worcestershire sauce, garlic, thyme, the almond flour mixture and salt and pepper to taste until well combined.
Form the meat mixture into a loaf shape, and place into a 9x13 baking dish.
Bake for 40 minutes.
While the meatloaf is baking, melt the butter in a skillet over medium heat.
Stir in the onions, and saute until well carmelized. Set aside.
Remove the meatloaf, and top it with the shredded cheese and caramelized onions.
Return the meatloaf to the oven, and bake for another 5-10 minutes, or until cooked completely through.