Preheat the oven to 325°F (160°C).
Heat the olive oil in a Dutch oven over medium-low heat. Add the sliced onions and cook for 15–20 minutes, stirring occasionally, until soft and lightly caramelized.
Add the garlic and cook for 1–2 minutes, until fragrant. Stir in the balsamic vinegar, cumin, smoked paprika, miso paste, molasses, Dijon mustard, and tomato paste. Cook for another 2 minutes, stirring constantly to prevent sticking.
Add the butter beans and stir to coat them in the sauce.
Pour in the vegan broth, diced tomatoes, and bay leaves. Bring to a gentle boil, then reduce the heat and simmer uncovered for 20 minutes.
Cover the Dutch oven with a lid and transfer to the oven. Bake for 90 minutes (1½ hours), until thickened and deeply flavorful.
Remove the bay leaves. Serve hot with toasted sourdough, vegan cheese, and chopped chives if desired.