Start by preheating your oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners for easy removal later.

In a medium bowl, whisk together the all-purpose flour, baking powder, baking soda, and salt. Set this mixture aside for later.

In a separate large bowl, beat the unsalted butter and granulated sugar together using an electric mixer until light and fluffy, about 3-4 minutes. This step is crucial for getting light, airy cupcakes.

Add the eggs one at a time, beating well after each addition. Then, stir in the vanilla extract. This will ensure the batter is smooth and creamy.

Gradually add the dry ingredients to the butter mixture, alternating with the whole milk. Start and end with the dry ingredients. Mix until just combined—don’t overmix, or your cupcakes may become dense.

Spoon the batter into the cupcake liners, filling each about two-thirds full. Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean. Let the cupcakes cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.

While the cupcakes are cooling, it’s time to make the custard filling. In a medium saucepan, heat the whole milk over medium heat until just simmering. In a separate bowl, whisk the egg yolks, sugar, and cornstarch together until smooth. Gradually pour the hot milk into the egg mixture, whisking constantly to avoid curdling. Return the mixture to the pan and cook, stirring continuously, until it thickens (about 3-5 minutes). Remove from heat and stir in the vanilla extract and butter. Let the custard cool to room temperature, then transfer to the refrigerator to chill for at least 30 minutes.

For the ganache, place the chopped semi-sweet chocolate in a heatproof bowl. In a small saucepan, heat the heavy cream over medium heat until it begins to simmer. Pour the hot cream over the chocolate and let it sit for 2 minutes. Stir until smooth and glossy. Allow the ganache to cool to room temperature before using.

Once the cupcakes have cooled, use a small knife or cupcake corer to create a small hole in the center of each. Spoon or pipe the custard filling into the hole, filling it generously.

Finally, spoon the cooled chocolate ganache over the filled cupcakes, allowing it to drip down the sides for a beautiful finish.