Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.

In a medium bowl, whisk together flour, baking powder, baking soda, salt, cinnamon, and nutmeg.

In a large bowl, cream butter and brown sugar until light and fluffy. Add eggs one at a time, beating well after each. Mix in vanilla.

Alternately add the dry ingredients and buttermilk to the creamed mixture, beginning and ending with the flour mixture. Mix until just combined.

Fold in chopped apples.

Divide batter evenly among cupcake liners. Bake for 22–25 minutes, or until a toothpick inserted in the center comes out clean.

Cool in pan for 5 minutes, then transfer to wire rack to cool completely.

While cupcakes cool, make the caramel sauce: In a saucepan over medium heat, combine brown sugar and butter. Stir until melted and bubbly. Add cream and salt, stir until smooth. Let cool slightly to thicken.

Spoon caramel sauce over cooled cupcakes. Sprinkle with flaky sea salt if using.