Preheat your oven to 300°F and set a kettle of water to boil—you'll need it later for the water bath. While the oven preheats, chop your bacon into bite-sized pieces and cook them in a skillet over medium heat for 4-5 minutes until they're crispy and rendered but not burnt. Transfer the cooked bacon to a paper towel to drain, then set aside. This early start allows the bacon to cool slightly before assembly and ensures your water is ready when you need it.
In a blender, combine the cottage cheese, shredded Gruyere cheese, cornstarch, salt, and black pepper. Blend on high speed until the mixture is completely smooth and creamy—this usually takes about 30-45 seconds. The cornstarch helps prevent the custard from becoming watery as it bakes. Add the eggs and blend again until fully incorporated and uniform. I like to do a quick taste test at this point to ensure the seasoning is balanced before baking.
Spray a standard 12-cup muffin tin generously with cooking spray, paying special attention to the corners where the bites are most likely to stick. Divide the cooked bacon from Step 1 evenly among the cups—aim for about 1-2 pieces per cup. Pour the custard mixture from Step 2 into each muffin cup, filling them about three-quarters full. The egg mixture will puff slightly during baking, so leave a little headroom to prevent overflow.
Place the filled muffin tin on a larger baking sheet or roasting pan. Carefully pour the boiling water from your kettle into the baking sheet until it reaches about halfway up the sides of the muffin cups—this creates a water bath that ensures gentle, even cooking and prevents the custard from curdling. Transfer the entire setup to your preheated 300°F oven and bake for 30 minutes. The egg bites are done when they're set around the edges but still slightly jiggly in the very center—they'll continue to cook slightly as they cool.
Remove the muffin tin from the oven first, then carefully lift it off the baking sheet and set it on a heat-safe surface to cool for about 5 minutes. This short rest allows the egg bites to firm up slightly without becoming rubbery. Run a small knife or offset spatula around the edges of each cup to loosen them, then gently pop them out onto a plate. I find that letting them cool for just a few minutes makes them much easier to remove cleanly without tearing.