Preheat oven to 400°.
Combine pinto beans, 2 tablespoons lime juice, cumin, and garlic in a blender; process until smooth, scraping sides. Set aside.
Combine remaining 1 tablespoon lime juice, tomato, and next 4 ingredients in a small bowl. Toss well, and set aside.
Place tortillas on a baking sheet; bake at 400° for 10 minutes or until crisp, turning after 5 minutes.
Place a large nonstick skillet coated with cooking spray over medium-high heat. Add bell pepper and onion. Coat vegetables with cooking spray; cook 6 minutes or until onion is tender. Stir frequently.
Spread 1/4 cup bean mixture on each tortilla. Divide tomato mixture evenly over bean mixture. Sprinkle each with 2 tablespoons cheese. Bake an additional 4 minutes or until cheese melts.