Mix wet ingredients: In a large mixing bowl, mix together wet ingredients. Stir until well combined. Let the oats soak in the mixture for 20 minutes to soften.
Preheat oven: While the oats are soaking, preheat oven to 350°F/180°C. Line a muffin pan with 9 muffin cups.
Mix dry ingredients: In a separate bowl, sift in whole wheat flour, baking powder, and baking soda. Add cinnamon, nutmeg, and salt and whisk to combine.
Combine: Add dry ingredients to wet and use a rubber spatula to gently fold together to form a thick batter. Sprinkle add-ins on top and fold the batter a few more times to distribute the add-ins.
Bake: Distribute batter among muffin cups, filling almost to the top. Place in the middle rack of the oven and bake for 35 minutes, or until a toothpick inserted in the center of a muffin comes out without any wet batter.
Cool: Place muffin pan on a wire rack. Let the muffins cool in the pan for 5 minutes, then carefully remove muffins from the pan. Place on wire rack to cool completely.
Store: Muffins can be stored at room temperature (in an airtight container) for the first 24 hours, then store in fridge for up to 3 more days.