Start by preheating your oven to 400°F and lining a baking sheet with parchment paper. Dice your potatoes into small, even cubes so they cook at the same rate. Toss the potatoes, bell peppers, and onion together in a mixing bowl with olive oil, garlic powder, smoked paprika, salt, and pepper until everything is evenly coated.
Spread the seasoned potato mixture in a single layer on your baking sheet, making sure nothing overlaps too much. Roast for about 25 to 30 minutes, stirring halfway through so every side gets a chance to crisp up. You want the edges golden brown and the centers fork-tender before pulling them out.
While the potatoes are roasting, crack your eggs into a bowl and whisk them well with a pinch of salt and pepper. Heat a non-stick skillet over medium-low heat and pour in the eggs, stirring gently and often. Cook them low and slow so they stay soft and fluffy instead of turning rubbery in the fridge later.
Once the potatoes are done and the eggs are scrambled, divide the potato mixture evenly among your meal prep containers as the base layer. Top each one with a portion of scrambled eggs and sprinkle shredded cheese over the top while everything is still warm. Let the bowls cool slightly before sealing the lids.
Let the assembled bowls sit uncovered for about ten minutes so steam doesn't build up inside the containers. Once they've cooled to room temperature, seal them and place them in the fridge. Wait to add salsa or any fresh toppings until you are ready to eat each bowl.