Add the eggs, cottage cheese, salt, and black pepper to a blender. Blend on high for about 30 seconds until the mixture is completely smooth with no lumps remaining.
Spray a 7-cup silicone egg bite mold generously with nonstick cooking spray. Divide the crumbled bacon and shredded gruyere cheese evenly among the cups.
Pour the blended egg mixture over the bacon and cheese, filling each cup almost to the top but leaving a tiny bit of room. Cover the mold tightly with aluminum foil.
Pour the water into the Instant Pot and place the trivet inside. Set the egg bite mold on top of the trivet. Lock the lid, set the valve to sealing, and cook on high pressure for 8 minutes.
When the cook time is done, let the pressure release naturally for 5 minutes, then carefully turn the valve to venting to release any remaining pressure. Remove the lid and carefully lift the mold out using the trivet handles or silicone tongs.
Remove the foil and let the egg bites cool in the mold for about 5 minutes. Gently pop them out onto a plate and serve warm.