Preheat the oven to 350°F (177°C). Line a 12-cup muffin pan with cupcake liners. Line a second pan with 2 liners—this recipe makes about 14 cupcakes. Set aside.

Whisk the flour, baking soda, baking powder, salt, cinnamon, and nutmeg together in a large bowl. Set aside.

Whisk the melted butter, brown sugar, and granulated sugar together in a medium bowl until combined. Whisk in the eggs and vanilla extract, then whisk in the milk. Slowly add the wet ingredients to the dry ingredients and stir gently until combined. The batter will have a few lumps. Fold in the apples.

Fill the cupcake liners ¾ of the way full with batter. Bake for 21–23 minutes, rotating the pan halfway through baking. A toothpick inserted in the center will come out clean when done. Remove from the oven and allow to cool completely before frosting.

Combine the butter and brown sugar in a saucepan over medium heat. Stir constantly as the butter melts.

Once melted, add 3 Tablespoons of heavy cream and the salt. Whisk to combine, then attach a candy thermometer and let the caramel boil until it reaches 230°F (110°C).

Remove from heat, whisk again, and let cool for 15–20 minutes before continuing.

Sift in confectioners’ sugar and add the remaining 2 Tablespoons of heavy cream. Beat on medium-low speed until incorporated, then increase to high speed and beat for 1 minute.

Let it sit for 20–30 minutes before filling your piping bag.

Frost cooled cupcakes and drizzle with salted caramel if desired.

Cover and store leftover cupcakes at room temperature for up to 1 day or in the refrigerator for up to 5 days.

Cupcakes can be made ahead 1 day in advance and stored at room temperature.

Frosted or unfrosted cupcakes can be frozen up to 3 months.