Preheat the oven to 325°F. Generously spray a silicone muffin tray with cooking spray. Place a pan of water on the bottom rack of the oven to create gentle steam and keep the egg bites soft.
If using onion, heat 1 tsp olive oil in a sauté pan over medium heat. Cook the onion until soft and translucent, about 5–6 minutes. Transfer to the blender. If using onion powder, skip this step and add it directly in Step 5.
Add a bit more oil if needed, then sauté the mushrooms until tender, about 5 minutes. Add the spinach and cook until wilted, 1–2 minutes. Remove from heat.
Add the cooked onions (or onion powder), eggs, cottage cheese, parmesan, hot sauce, salt, and pepper to the blender and blend until smooth and creamy.
Pour the blended mixture into a mixing bowl and fold in the mushroom–spinach mixture.
Divide evenly into the muffin cups.
Bake 28–32 minutes until the centers are set. Cool for 5 minutes before removing.