Preheat your oven to 350°F. Prepare a silicone muffin pan by coating it lightly with cooking spray and place it on a baking sheet for added stability.
In a large skillet, heat the olive oil over medium heat. Add the onion and red bell pepper, and sauté for about 4-5 minutes until they are softened. Stir in the spinach and cook for an additional 2 minutes until wilted. Remove from heat and let cool slightly.
In a large mixing bowl, whisk together the eggs, cottage cheese, Dijon mustard, garlic powder, and black pepper until the mixture is smooth.
Gently fold the cooled vegetables, shredded cheese, and bacon bits into the egg mixture until everything is just combined.
Spoon the mixture evenly into the prepared muffin cups, filling them about three-quarters full. Bake in the preheated oven for 25-30 minutes or until the bites are set and lightly golden on top.
Allow the bites to rest for 10 minutes before carefully removing them from the pan. Serve warm, garnished with chopped chives or green onions if desired.