Preheat the oven to 350 degrees F.
Grease a 12-cup muffin tin with cooking spray.
Line each cup with a slice (or two) of ham, depending on how thin your ham is sliced by placing individual ham slices over each muffin cup and gently press down in the middle until a cup shape forms.
In a blender, combine the eggs, cottage cheese, salt, and pepper and blend until smooth. Stir in the spinach and green onions.
Ladle about ¼ cup of the egg mixture into each of the cups. Top with the shredded cheese.
Transfer to the middle rack of the oven and bake until the eggs have just set, about 15 minutes.
Remove from the oven and let cool slightly in the muffin tin, about 5 minutes. To remove from the muffin tin, I carefully loosen up the edges using a mini-silicone spatula or butter knife around the edges of the cooked egg bite, then carefully lift out. Serve immediately or if preparing for meal prep- transfer to a wire rack and let cool completely before storing in an air tight container. These keep well for 3-5 days in the fridge.