Place the beans in a large bowl or pot and cover by at least two inches of cool water. Soak the beans at room temperature for at least 6 hours and up to overnight. Drain and rinse beans.
Place the drained beans in a large saucepan and cover by at least two inches with water. Stir in 2 teaspoons salt. Bring to a boil over high heat, then reduce heat to medium-low and simmer, covered, for 30-40 minutes, until the beans are tender but not mushy. Drain, reserving the liquid.
Preheat the oven to 375°F. If necessary, rearrange the oven racks to make room for a pot or Dutch oven.
Place the bacon in an oven-safe Dutch oven or similar large pot with a lid (if you don’t have a lid, you can use a double sheet of aluminum foil). Saute over medium to medium-low heat until the fat is rendered and the bacon is crisp, about 8 minutes, adjusting the heat as needed so the bacon does not burn. Add the onion and garlic and cook, stirring, until the onion is softened, about 5 minutes.
Add the beans, molasses, tomato paste, and mustard. Stir to combine, then stir in 2 cups of the reserved bean cooking water.
Cover the pot and carefully transfer it to the oven. Bake until the beans are nice and soft and ultra flavorful, about 3 hours. Check the beans every 45 minutes or so and add more bean cooking liquid (or water if you run out) if the beans are drying out.
Remove the pot from the oven. Stir in the vinegar and season to taste with salt and pepper. Cool for 5-10 minutes before serving.
No-Soak Method:
Preheat the oven to 325°F. If necessary, rearrange the oven racks to make room for a large pot or Dutch oven.
Place the bacon in an oven-safe Dutch oven or similar large pot with a lid (if you don’t have a lid, you can use a double sheet of aluminum foil). Saute over medium to medium-low heat until the fat is rendered and the bacon is crisp, about 8 minutes, adjusting the heat as needed so the bacon does not burn. Add the onion and garlic and cook, stirring, until the onion is softened, about 5 minutes.
Add the beans, molasses, tomato paste, mustard, and salt and stir well to combine. Add 4 cups of water, stir, turn the heat to high, and bring to a boil. Reduce the heat to low, partially cover the pot, and simmer for 30 minutes. Cover the pot and carefully transfer to the oven.
Cook until the beans are soft, 4-5 hours. Check every 45 minutes to stir and add more water if the beans are not fully covered.
Add the vinegar, and season to taste with salt and pepper. Cool for 5-10 minutes before serving.
Notes
TO SWAP CANNED BEANS: Instead of dried beans, substitute 2 (15-ounce) cans of white beans (such as cannellini) that are rinsed and drained. Saute the bacon, onion, and garlic in a large pot or Dutch oven as directed. Add 2 cups water, the beans, and all of the remaining ingredients except for the vinegar. Cover at bake at 375°F until the beans are soft and the mixture is thickened about 40-60 minutes, depending on the size of your pot (wider pots will evaporate liquid more quickly). Stir in the vinegar and salt and pepper to taste.
TO STORE: Refrigerate Boston baked beans in an airtight container for up to 4 days.
TO REHEAT: You can reheat your beans in the microwave, or in a pan set over medium-low heat.
TO FREEZE: Transfer Boston baked beans to an airtight container or freezer bag and freeze for up to 3 months. Let them thaw in the refrigerator before reheating according to the instructions above.