Preheat the Oven: Preheat your oven to 400°F (200°C). Line a baking sheet with parchment paper.
Roast the Potatoes and Onions: Place the diced potatoes and onions on the prepared baking sheet. Toss with olive oil, salt, and smoked paprika. Bake at 400°F for 15 minutes.
Prepare the Egg Mixture: While the potatoes are roasting, lower the oven temperature to 350°F (175°C). Spray a 12-cup muffin tin with cooking spray. In a high-speed blender, combine the eggs, cottage cheese, onion powder, and a pinch of salt. Blend until completely smooth.
Assemble the Bakes: Distribute the roasted potatoes and onions evenly into each muffin cup. Pour the egg mixture on top, filling each cup about ¾ full. Stir gently to mix the egg mixture and potatoes.
Add Cheese and Chives: Sprinkle the shredded cheddar cheese and diced chives evenly over the top of each bake.
Bake: Bake at 350°F for 18-20 minutes, or until the egg mixture is set and the cheese is melted and golden brown. For the last minute or two, switch the oven to broil to brown the cheese even more (watch carefully to prevent burning!).
Cool and Serve: Allow the bakes to cool slightly in the muffin tin before serving.