Lay tortillas on a work surface. Spread peppers and onions on half of each tortilla, dividing evenly. Top with cheese, dividing evenly. Fold the tortillas in half, pressing gently to flatten.
Heat a large griddle or skillet over medium heat. Cook 2 of the quesadillas until crispy on the outside and the cheese is melted, 2 to 4 minutes per side. Repeat with the remaining 2 quesadillas. Let the quesadillas cool for 1 minute before cutting into wedges to serve. Serve with guacamole and salsa.