Prep the peppers: Slice off the tops, remove seeds and membranes, and trim the bottoms slightly if needed so they stand upright. Brush the outsides lightly with olive oil.
Preheat the air fryer: Set to 360°F (182°C) for 3 minutes so the basket is warm and ready.
Sauté aromatics: In a skillet over medium heat, add 1 tablespoon olive oil.
Cook onion for 3–4 minutes until soft, then add garlic for 30 seconds until fragrant.
Build the filling: Stir in tomatoes, tomato paste, cumin, smoked paprika, oregano, and red pepper flakes. Cook 2 minutes to thicken slightly.
Mix it all together: Add quinoa, black beans, and corn. Season with salt and pepper.
Remove from heat and fold in 1/2 cup shredded cheese.
Stuff the peppers: Spoon the filling into each pepper, packing it in gently. Top with a little extra cheese.
Air fry, round one: Arrange peppers upright in the basket (work in batches if needed). Air fry at 360°F (182°C) for 10–12 minutes until peppers are tender and cheese is melted.
Brown the tops: Increase heat to 380°F (193°C) for an additional 2–4 minutes to get a golden, bubbly top.
Watch closely to avoid over-browning.
Finish and serve: Let rest 2 minutes. Garnish with cilantro or parsley. Serve with lime wedges or a spoon of Greek yogurt if you like.