In large Dutch oven or pot, heat olive oil over medium heat. Add tomato paste and shallots and cook, stirring frequently, until shallots are soft and tomato paste has darkened, about 5 minutes. Add garlic and thyme and cook, stirring continuously, until fragrant, about 1 minute.
Add vegetable stock, pepper, and salt. Cover with lid and bring to boil. Once boiling, reduce the heat to medium-low and simmer for 5 minutes to let the flavors meld.
Pour beans into pot and gently stir to mix. Cover with lid and cook over medium-low heat until the beans are warmed through, about 10 minutes. Stir in miso until fully dissolved.(It’s okay if some beans get squished while doing this—it’ll thicken the broth.) Stir in the Swiss chard. Taste and season with more salt, if needed.
Serve the beans hot with lemon on the side and bread for dipping, if using.