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 diced 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. (However, note that the sauce will thicken a bit upon standing).
Garnish with chopped parsley, if desired.
2 tablespoons chopped parsley, for garnish
Notes
Taste the sauce before pouring it over the beans. Adjust the seasoning if needed, adding more salt, pepper, or sweetness according to your preference.
In a hurry? Use a store-bought BBQ sauce as a substitute for the molasses, ketchup, brown sugar, soy sauce, and vinegar.
Use canned navy beans instead of dried ones to skip the soaking and long cooking process. Rinse and drain them before use.
Use frozen diced onions to save time on chopping. Or use 1 tablespoon of onion powder if you prefer not to use fresh or frozen onions.
No liquid smoke? Use ½ teaspoon of smoked paprika, or smoked salt instead of the regular salt, to add that smoky flavor.
Use additional brown sugar or some maple syrup as a substitute for molasses. It won't be as rich, but it will still add sweetness.
You can add diced carrots, celery, and bell peppers for extra nutrition and color. Include some mushrooms for more of a meaty texture. Or add cubed, marinated tofu or tempeh for a protein boost.
Add spices like smoked paprika, cumin, or chili powder for a different flavor profile.
Add a pinch of cayenne pepper, red pepper flakes, or diced jalapenos for a spicy kick.
To change up the sweetness profile, you can use maple syrup or honey instead of the brown sugar.
Replace some of the water with beer (such as a stout or porter) for a deep, malty flavor. Or use vegetable or chicken broth instead of water for added depth of flavor.
Top the finished dish with crispy fried onions, breadcrumbs, or crushed tortilla chips before the final baking stage to add a nice crunch.
Recipe slightly adapted from Vegan Beans from Around the World.