Preheat your oven to 300F. Generously grease a 12-cup muffin tin with cooking spray or butter. Place a kettle of water on to boil for the water bath.
Add the eggs, cream cheese, and cottage cheese to a blender. Blend on high for about 30 seconds until completely smooth and frothy with no lumps remaining.
Pour the blended mixture into a large bowl. Fold in the shredded gruyere, chopped smoked salmon, chives, dill, salt, and black pepper until evenly combined.
Divide the mixture evenly among the 12 muffin cups, filling each about three-quarters full.
Sprinkle the top of each egg bite with everything bagel seasoning, dividing it evenly.
Place the muffin tin inside a larger baking pan. Carefully pour the boiling water into the larger pan until it reaches about halfway up the sides of the muffin tin. This water bath is what gives the egg bites their signature silky, custard-like texture.
Bake for 30 to 35 minutes, until the egg bites are set and just slightly jiggly in the center. They will firm up as they cool.
Let the egg bites cool in the tin for 5 minutes, then run a small spatula around the edges and gently pop them out. Serve warm or store in the fridge for easy meal prep.
