Preheat your oven to 350°F (177°C) and line a muffin tin with cupcake liners.

In a large mixing bowl, combine all-purpose flour, baking powder, baking soda, salt, ground cinnamon, and ground nutmeg. Whisk together until well blended, about 2 minutes.

In a separate bowl, beat the melted unsalted butter and granulated sugar together until light and fluffy, about 3-4 minutes. Add the large eggs one at a time, mixing well after each, then stir in the vanilla extract.

Gradually add the dry ingredients to the wet mix, alternating with the whole milk. Start and finish with the dry ingredients, mixing gently.

Spoon the batter into prepared cupcake liners, filling each about two-thirds full, and bake for 18-22 minutes or until a toothpick comes out clean.

In a medium bowl, mix together light brown sugar, pure maple syrup, and toasted pecans for the filling.

Once the cupcakes cool, fill each with the pecan filling using a small spoon.

To make the frosting, beat the cream cheese and powdered sugar until silky smooth.

Frost each cooled cupcake with the cream cheese frosting and drizzle with caramel-pecan glaze.