Whisk together 1/2 cup milk with the eggs, cornstarch, protein powder, stevia, and salt in a medium bowl; set aside.
Pour the remaining 2 cups of milk into a heavy-bottomed medium saucepan over medium heat. Cook until bubbles form around the outside and the milk starts to steam.
Turn off the heat and very slowly whisk 1 cup of hot milk into the egg mixture, starting with just a couple drops at a time and gradually adding more until the whole cup is incorporated.
Pour this into the pot and bring to a boil over medium-low heat, stirring constantly. Once boiling, turn off heat and stir in the vanilla, nutmeg, and cinnamon.
Strain through a fine mesh sieve to remove any lumps, then pour into small, individual-sized serving bowls or cups.
Cool to room temperature, and then refrigerate to chill.
Before serving, top each with whipped topping and a sprinkle of nutmeg.