Heat oven to 425° F. Heat the oil in a large skillet over medium-high heat. Add the peppers, onions, 1 teaspoon salt, and ½ teaspoon pepper. Cook, stirring frequently, until soft, 20 to 25 minutes. Add the beans and cheese and stir to combine.
Heat another large skillet (preferably cast-iron) over medium-high heat. Toast the tortillas one at a time until browned in spots, 30 seconds per side. Place the filling on one side of each tortilla, dividing evenly. Fold the other side of each tortilla over the filling. Bake on 2 large rimmed baking sheets until the cheese is melted, 10 to 12 minutes.
Cut each quesadilla into wedges and serve with the Pico de Gallo.
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