Place 1⅓ cups dried navy beans in a large bowl that can be fitted with a lid. Pour fresh water over the beans until the water is at least 1 inch above the beans. Seal the container shut. Soak at room temperature for 8-12 hours.
After soaking, drain the beans. Add the soaked beans to a large stock pan. Add enough fresh water to cover beans by 1 inch. Bring water to a rapid boil then reduce to a simmer. Simmer for 1 hour or until beans are tender but not falling apart. Drain cooked beans well.
Alternatively, you can speed up the process by cooking the soaked beans in the Instant Pot after they have been soaked (Navy beans' texture is best if soaked before cooking.)
For the Baked Beans
Preheat oven to 300℉ (150℃).
Heat a large skillet over medium-high heat. Add in the diced bacon and cook until bacon begins to render fat and then stir in the minced onion. Sauté bacon and onions together until onions begin to soften and the bacon is browned and slightly crisp. This should take about 5-6 minutes. After browned, drain off the excess grease that the bacon has rendered.
In a large bowl, mix together ½ cup tomato sauce, ¼ cup molasses, ¼ cup brown sugar, ¼ cup pure maple syrup, 1 teaspoon kosher salt, 2 teaspoons dried mustard, 1 tablespoon apple cider vinegar, ½ cup apple juice, and ½ cup water until well combined. Gently fold in the beans, bacon, and onions.
Pour the bean mixture into a 2-quart oven-safe dish. Beans should be pretty well submerged in liquid and the mixture should be relatively loose. If there does not seem to be enough liquid in the baking dish, add up to ½ cup of additional water or juice. Cover the pan with foil or an oven-safe lid.
Bake covered for 2 hours. After 2 hours, remove the lid or foil, and bake for another 30-60 minutes, or until thickened.
Notes
***Old dried beans may take longer to cook and never fully soften.*** It is best to use dried beans within 6 months of purchase and ALWAYS check the expiration date — even recently purchased beans may have been in storage for a while.Type of Beans: Navy Beans are traditional for baked beans, but pinto beans or Great Northern beans can be used in a pinch. Using Canned Beans: In place of dried beans, you can use 4 cups of canned navy beans, rinsed and drained (measure after draining -- you will need about three 15-ounce cans). I would also add just a pinch of salt or omit it altogether. Dried Mustard: In place of dried mustard, feel free to use 1 tablespoon of prepared mustard.Sweeter Baked Beans: For really sweet baked beans, use ketchup in place of the tomato sauce OR add up to ½ cup brown sugar instead of ¼ cup brown sugar. Vegetarian Baked Beans: Omit the bacon and add the onions raw to the bean mixture. You will want to add an additional ½ teaspoon of kosher salt to the bean mixture, as the bacon has quite a bit of sodium. Storage: Let the baked beans cool fully, then store in an airtight container in the refrigerator for up to 5 days or freeze in a freezer-safe container for up to 3 months. Thaw frozen beans overnight in the refrigerator, then reheat covered at 300°F for about 45 minutes, or microwave in 60-second intervals until warmed through.