Collect all the necessary ingredients, ensuring everything is ready before you begin. This step helps streamline the cooking process and ensures you have everything on hand.
In a bowl, sift the flour, nutmeg, salt, and pepper together. In a separate medium bowl, beat the eggs, then gradually mix in the milk and the sifted flour mixture, alternating between the two, until the batter is smooth. Allow the mixture to rest for 30 minutes to thicken and develop its texture.
Bring a large pot of gently salted water to a boil. Using a spaetzle press, press the batter into the boiling water, allowing the small dumplings to form and cook.
Once the spaetzle rises to the surface of the water, use a slotted spoon to carefully lift it out and transfer it to a bowl.
Stir in 1 cup of cheese, blending it thoroughly until it melts and coats the spaetzle evenly.
Heat butter in a large skillet over medium-high heat until melted. Add the onion and cook, stirring occasionally, until it turns golden brown. Stir in the spaetzle and the remaining ½ cup of cheese, mixing until everything is well combined. Remove from heat and serve right away for a deliciously warm dish.