Preheat the oven to 325°F. Grease a 12-cup muffin tin generously to prevent sticking.
In a large bowl, whisk eggs until smooth.
Fold in cottage cheese, bacon bits, shredded cheese, salt, and black pepper. Mix well.
Pour the egg mixture into the muffin cups, filling them about ¾ full.
Place a small pan of water on the lower rack of the oven. This helps keep the egg bites moist.
Bake for 23-25 minutes or until the centers are set. A toothpick inserted should come out clean.
Let them cool in the muffin tin for 2-3 minutes before carefully removing.
Serve warm and enjoy!