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Clean beans and soak them overnight in a bowl or big pot. About 2" water.
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After 24 hours drain the water and cover the beans with an equal amount of water. Bring to a boil, then reduce heat to low, cover the pot, and let simmer for 1 hour. Drain beans, reserving liquid.
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In a large oven safe pot, Dutch oven or baking dish, combine soaked beans, 1 cup cooking water, onion, ketchup, brown sugar, molasses, salt, mustard, pepper and bay leaf.Mix well.Cover and bake for 4 1/2 hours or until beans are very tender and sauce has thickened to desired consistency. Stir occasionally and add more of the reserved cooking liquid if needed during cooking time.
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At end of cooking time remove and discard bay leaf. Taste beans and season with additional salt and pepper, if needed.
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Alternatively you can use a slow cooker. After boiling the beans, add the rest of the ingredients to a slow cooker. Cook on LOW for 7-9 hours or on HIGH for 3-4 hours, stirring occasionally. If the beans are too thick, stir in a little cooking water, if not thick enough, continue to cook.