Drain soaked beans and place in a large pot. Cover with fresh water, bring to a boil, then simmer for 1 hour.

Preheat oven to 300°F (150°C). Drain beans and transfer to a baking dish.

Stir in molasses, brown sugar, onion, ketchup, mustard, salt, and pepper.

Pour water over the mixture until beans are just covered. Lay bacon slices on top (if using).

Cover and bake for 5–6 hours, stirring occasionally and adding water if needed.

Uncover for the last 30 minutes to thicken the sauce. Serve hot!