Place the beans in a pot over medium-high heat and cover them with about an inch of water. Bring to a boil, then reduce the heat and simmer until the beans are tender, about an hour.
2 cups navy beans
Preheat the oven to 325 degrees F (160 degrees C).
Combine the molasses, salt, pepper, mustard, ketchup, brown sugar, soy sauce, apple cider vinegar, and liquid smoke in a pot, and bring to a boil over medium heat.
3 tablespoons molasses, 2 teaspoons salt, ¼ teaspoon black pepper, ½ teaspoon dry mustard, ½ cup ketchup, ½ cup brown sugar, 2 teaspoons soy sauce, 1 teaspoon apple cider vinegar, 1 teaspoon liquid smoke
Drain the beans and place in a casserole dish with the onion. Pour the molasses mixture over the beans and then add water so that the beans are just covered with liquid.
¾ cup finely chopped yellow onion
Cover the casserole dish and bake about 3 - 3 ½ hours, checking periodically to make sure the beans aren't drying out.
If the liquid isn't quite thick enough, remove the cover and bake for another 15 minutes
Notes
Recipe slightly adapted from Vegan Beans from Around the World