Sift flour, nutmeg, salt, and pepper in a bowl.
Beat the eggs in a medium bowl. Gradually add the flour and milk, one at a time. The batter should resemble a thick pancake batter. If it is too thick, add more milk, a tablespoon at a time. If it is too loose, add in a little more flour, a tablespoon at a time. Let the batter rest for 30 minutes.
Bring a large pot of lightly salted water to a boil. Spoon the batter into the spätzle maker and drip into the boiling water. You can use the scraper to help move the batter through the spätzle maker as needed.
When all the spätzle has floated to the top of the water and is firm to the touch, remove it with a slotted spoon and place it in a bowl for assembly.