Preheat the oven
Preheat oven to 325°F and prepare all the ingredients.
Cook the bacon
Put the diced bacon into a cold cast-iron or nonstick skillet. Warming over medium heat, sauté for 8 to 10 minutes, stirring often, until the bacon is fully cooked but not overly crispy. When finished, take the skillet off the heat and move the bacon to a plate lined with paper towels to soak up excess grease. Save the rendered bacon fat to use later.
Prepare the egg mixture
In a blender or using an immersion blender, blend together the eggs, softened cream cheese and kosher salt. Blend for 15 to 20 seconds, until frothy and fully emulsified.
Grease the muffin tin
Very generously smear the reserved bacon fat in each well of a muffin tin with a paper towel. This makes removing the egg bites easy as well as adding more flavor.
Fill the muffin wells
Divide the cooked bacon and shredded Gruyère cheese evenly among the 12 muffin wells. Now pour egg mixture into each well, approx three-quarters full. With a butter knife, gently incorporate the bacon, cheese and eggs in each well. Season well with freshly ground black pepper, to taste, on top.
Bake the egg bites
Put the muffin tin in the oven and bake for 16 to 20 minutes. Halfway through, rotate the tin from front to back for even cooking. The egg bites should be set on the edges, but might still jiggle a bit in the center. This is normal; they will set up as they cool.
Remove and serve
When baked, take the tin out of the oven. Using a butter knife, carefully loosen the egg bites from around the edges of the wells. Allow to cool slightly before serving. To store, let the bites cool completely before placing in an airtight container. They can be stored in the refrigerator for up to five days.