Dice the onion, bell pepper, and jalapeno pepper. Mince the garlic.
In a large pot, heat the olive oil over medium-high heat. Add the diced onions and red bell pepper and sauté for 2-3 minutes.
Add the chopped jalapeno, garlic, chili flakes, black pepper, cumin, chipotle pepper and its juice. Stir and sauté for 1 minute.
Add the vegetable broth, black beans, and bay leaf. Stir and bring to a boil over high heat.
Once boiling, reduce the heat to low, cover with a lid, and simmer for 15 minutes.
Remove the bay leaf. Blend about 2 cups of the soup (with a blender or immersion blender) and pour back into the pot. Season with salt to taste and adjust any of the seasonings if needed.
Garnish with lime juice, cilantro, sour cream, avocado, jalapeno, and tortilla chips. Serve with crusty bread, tortilla chipas, or side salad.