Preheat oven to 375 degrees F (190 degrees C). Grease 12 muffin cups.
Mix almond milk, applesauce, apple, raisins, pecans, flax meal, eggs, brown sugar, cinnamon, and nutmeg together in a bowl; stir in oats until well mixed. Let sit for 5 minutes. Scoop mixture into the prepared muffin cups using an ice cream scoop.
Bake in the preheated oven until lightly browned, about 20 minutes. Let oatmeal sit in muffin tin for 5 minutes before transferring to a wire rack to cool completely.