In a medium soup pot over medium heat, add olive oil. Add the onion, carrots, bell pepper, garlic, chili powder, cumin, and black pepper. Cook stirring for about 15 minutes or until vegetables are soft and tender. Stir in the chipotle.
Turn the heat to high and add the tomatoes and their juice. Bring to a boil, stirring and crushing the tomatoes. Reduce the heat and simmer for about 20 minutes.
Add the lentils, beans, 14 oz. of water, and salt to the pot. Bring to a boil, lower the heat and simmer for another 20 minutes. Add more water if it gets too thick.
Serve with chopped cilantro.