Preheat your oven to 350°F (175°C). In a large mixing bowl, whisk together the all-purpose flour, baking powder, baking soda, salt, ground cinnamon, and ground nutmeg until well combined.

In a separate bowl, beat the melted butter and granulated sugar until fluffy for about 3-4 minutes. Gradually add the eggs one at a time, mixing well after each addition. Stir in the pure vanilla extract.

Alternately incorporate the dry mixture with the whole milk until just combined for a smooth batter.

Line a muffin tin with cupcake liners and fill each about two-thirds full with the batter. Bake for 20-25 minutes, or until a toothpick comes out clean. Let the cupcakes cool in the tin for 5 minutes before transferring to a rack.

Combine the light brown sugar, pure maple syrup, and additional melted butter in a medium saucepan over medium heat. Stir until it bubbles gently, then add toasted pecans.

Cook, stirring, for about 3-4 minutes until the filling is gooey and caramelized. Remove from heat and let cool slightly.

Create a hollow in the center of each warm cupcake and spoon a generous amount of the pecan filling into each cupcake.

Top each filled cupcake with cream-cheese frosting. Drizzle warm caramel sauce over the frosted cupcakes.

Lightly brush the tops of the cupcakes with more caramel sauce for a glossy shine. Allow to set before serving.