Preheat the oven to 350°F. Lightly grease a 6-cup muffin tin with avocado or olive oil spray.
Heat the ghee in a skillet over medium heat. Once hot, add the zucchini, red onion, and bell pepper.
Sauté for 3–4 minutes, stirring occasionally, until the vegetables have softened and released some moisture. Remove from heat and let cool slightly.
In a blender, combine the eggs, cottage cheese, and milk. Blend until smooth and frothy, about 20–30 seconds. Transfer the mixture to a bowl and stir in ½ cup shredded cheddar, garlic powder, and a pinch of sea salt.
Spoon the sautéed vegetables evenly into the bottom of each muffin cup so every bite gets a similar amount. Pour the egg mixture over the top, filling each cup about three-quarters full. Sprinkle with additional cheddar and a pinch of chives or green onion. Option to finish with a few cracks of black pepper on top.
Bake for 18–20 minutes, or until the egg bites are puffed, set in the center, and lightly golden on top. A toothpick inserted in the center should come out clean.
Let the bites cool for 5 minutes before running a knife around the edges to release. Serve warm. Enjoy!