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 3/4 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.

(This frosting is popular, so we have a separate salted caramel frosting post if you need more help making it.) Combine the butter and brown sugar in a saucepan over medium heat. With a rubber spatula or wooden spoon, stir constantly as the butter melts. Once butter has melted, switch to a whisk to make sure the two are really combined. (Otherwise, you might see an oily layer around the edges where they’re still a bit separated; you do not want that.) Once melted butter and brown sugar are combined, add 3 Tablespoons of heavy cream and the salt. Whisk to combine, then stop whisking and attach a candy thermometer to your pan, making sure the bulb is not touching the bottom of the pan. Let the caramel boil, giving it a quick whisk every 30 seconds or so, until the temperature reaches 230°F (110°C). On my stove, it takes just under 2 minutes.

Remove the saucepan from heat, give it another quick whisk, and let cool for a minute. Carefully transfer the salted caramel to a heat-proof mixing bowl set on a cooling rack and cool for just 15–20 minutes before continuing. The caramel sauce thickens during this time.

Sift in confectioners’ sugar and add remaining 2 Tablespoons of heavy cream. With a handheld or stand mixer fitted with a whisk attachment, beat on medium-low speed until the ingredients are incorporated. Turn mixer up to high speed and beat for 1 minute. Avoid over-mixing or the frosting will begin to “break” and separate. Let it sit for at least 20–30 minutes before filling your piping bag, to give it a chance to thicken up to a pipeable consistency.

Frost cooled cupcakes and drizzle with salted caramel, if desired. I used Wilton 2A piping tip on the pictured cupcakes.

Cover and store leftover cupcakes at room temperature for up to 1 day or in the refrigerator for up to 5 days. I recommend a cupcake carrier for storing and transporting decorated cupcakes.