Preheat your oven to 350°F (175°C). Line a muffin tin with cupcake liners and set aside. This ensures your cupcakes bake evenly and don’t stick.
In a large bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, baking soda, salt, cinnamon, and nutmeg until well combined. This helps distribute the spices and leavening agents uniformly.
In a separate bowl, beat the granulated sugar, brown sugar, and vegetable oil until the mixture is smooth and slightly fluffy. Add the eggs one at a time, beating well after each addition. Stir in the vanilla extract and apple cider.
Gradually add the dry ingredients to the wet ingredients, folding gently with a spatula until just combined. Avoid overmixing to keep your cupcakes tender and light.
Divide the batter evenly among the cupcake liners, filling each about two-thirds full. Bake for 18-22 minutes or until a toothpick inserted into the center comes out clean.
Remove cupcakes from the oven and let them cool in the tin for 5 minutes before transferring them to a cooling rack. Allow the cupcakes to cool completely before frosting.
In a mixing bowl, beat the softened unsalted butter until creamy. Gradually add powdered sugar, beating until smooth. Add apple cider vinegar and cinnamon, then mix until fully incorporated. Adjust consistency with a teaspoon of water if needed.
Once the cupcakes are cool, frost them with your prepared frosting using a knife or a piping bag for a decorative touch. Sprinkle a little extra cinnamon on top for garnish if desired.