Preheat the oven
Set your oven to 325°F to allow it to fully preheat while preparing the egg bites.
Cook the bacon
Place the diced bacon in a cold cast-iron or nonstick skillet and heat it over medium heat. Stir the bacon frequently as it cooks for 8 to 10 minutes, ensuring it becomes fully cooked without becoming overly crispy. Remove the skillet from the heat and transfer the bacon to a plate lined with paper towels to drain. Retain the rendered bacon fat for later use.
Prepare the egg mixture
Combine the eggs, softened cream cheese, and kosher salt in a blender or with an immersion blender. Blend the ingredients for approximately 15 to 20 seconds until the mixture becomes frothy and fully emulsified.
Grease the muffin tin
Using a paper towel, generously coat each well of a muffin tin with the reserved bacon fat. This step helps to prevent sticking and adds an additional layer of flavor.
Fill the muffin wells
Distribute the cooked bacon pieces and shredded Gruyère cheese evenly among the 12 greased wells. Carefully pour the egg mixture into each well, filling them about three-quarters full. Use a butter knife to gently combine the bacon, cheese, and eggs within each well. Sprinkle a liberal amount of ground black pepper on top.
Bake the egg bites
Place the muffin tin in the oven and bake for 16 to 20 minutes. Rotate the pan halfway through to ensure even cooking. The egg bites should be set on the outer edges but may remain slightly jiggly in the center, which is normal as they will firm up while cooling.
Remove and serve
Take the egg bites out of the oven and run a butter knife around the edges of each well to loosen them. Allow them to cool slightly before serving warm. For storage, let the egg bites cool completely, then place them in an airtight container and refrigerate for up to five days.