First, preheat your oven to 320°F (160°C). Ensuring your oven is at the correct temperature from the start is crucial for an even bake. While it heats up, line a standard 12-cup muffin tin with paper liners to prevent sticking.
In a large mixing bowl, beat the room-temperature cream cheese, sugar, milk, and melted unsalted butter together. Mix on medium speed until the mixture is completely smooth and creamy, with no lumps remaining. This forms the rich foundation of your cupcakes.
Add the egg yolks to the cream cheese mixture one at a time. Be sure to mix well after each addition until it is fully incorporated. This step enriches the batter and contributes to the final custard-like flavor of the cheesecake cupcakes.
In a separate, clean, and dry bowl, use an electric mixer to whip the egg whites. Start on low speed and gradually increase to high. Whip until soft peaks form—this means when you lift the beaters, the peaks gently curl over.
Now, carefully fold the whipped egg whites into the cream cheese batter. Use a spatula to gently scoop from the bottom and fold over the top. Do this in two or three additions to maintain as much air in the batter as possible.
Sift the all-purpose flour and salt directly into the batter. Continue to fold gently until the flour is just combined. Overmixing at this stage will deflate the egg whites and result in dense cupcakes, so be careful to mix just enough.
Carefully pour or spoon the batter into the prepared muffin liners, filling each one about two-thirds full. This leaves enough room for the cupcakes to rise beautifully in the oven without spilling over the sides of the liners.
Bake for 20-25 minutes. The cupcakes are done when the tops are a light golden brown and a toothpick inserted into the center comes out clean. Let them cool in the tin for 10 minutes before moving them to a wire rack.