Place oven rack in the middle row. Preheat oven to 350 degrees F (175 degrees C). Grease 12 muffin cups.
Combine eggs, butter, water, and sea salt in a bowl. Sift almond flour, flax meal, and baking soda into egg mixture while continually stirring. Add Cheddar cheese and thyme; stir until batter is well combined. Spoon batter into the prepared muffin cups. Sprinkle extra Cheddar cheese over each muffin.
Bake in the preheated oven until golden on top, 13 to 14 minutes.