Heat 2 tablespoons oil in a Dutch oven or large pot over medium-high heat until shimmering.
Add the chopped onions and cook, stirring occasionally, until softened, about 5 minutes.
Stir in the minced garlic and cook until fragrant, about 30 seconds.
Add the soaked, drained black beans to the pot along with 2 chipotle chilies, 2 teaspoons adobo sauce, 1 teaspoon ground cumin, 1 teaspoon dried oregano, and 2 bay leaves.
Pour in about 6 cups water or enough to cover the beans, stir to combine, and bring to a boil over medium-high heat.
Reduce heat to low, cover, and simmer until the beans are tender, about 1½ to 2 hours, stirring occasionally and adding more water if needed to keep beans covered.
Remove from heat. Optionally remove the chipotle chilies and bay leaves, then stir in lemon and lime juice and season to taste with salt and freshly ground black pepper.