Place the dried navy beans in a 4-quart (4 L) Dutch oven. Cover the beans with cold water and let them soak for eight hours or overnight.
Rinse & Cook The Beans (45 minutes)
Drain and rinse the beans with cool water. Place the drained beans back in the Dutch oven and cover them with 6 cups (1 ½L) of fresh cold water. Bring the beans to a light boil over medium-high heat. Once bubbling, add the baking soda. Reduce the heat, place the lid on the pot, and simmer the beans for 30 minutes or until tender.
Bake The Beans (8 hours)
Preheat the oven to 250ºF (120ºC).
Drain the cooked beans into a colander fitted over a large bowl or another vessel to catch the liquid. Once drained, you should have about 3 ½ cups (875 ml) of cooking liquid (if you don't have 3 ½ cups, top it up with water until you do).Rinse the cooked beans with cool water and drain. Set the cooking liquid and the drained beans aside.
Give the Dutch oven a quick wash to remove any cooked on bean scum. Add the ketchup, molasses, apple cider vinegar, brown sugar, ground dry mustard, and pepper to the pot. Stir together until smooth.
Add the chopped onion and bacon to the pot. Add the 3 ½ cups of reserved bean liquid and the cooked beans. Stir well to combine.
Place the lid on the Dutch oven and transfer the pot to the preheated oven. Bake the beans for 8 hours (I usually bake mine overnight). Remove the baked beans from the oven, remove the lid, stir, and serve.
Notes
When boiling the beans, keep the heat at a low bubble to prevent them from breaking apart. Rapid boiling can cause the beans to become mushy and may affect the texture of the final dish.
If your beans are watery when you take them out of the oven after baking, don’t worry! They will thicken as they cool. If your beans don’t thicken, preheat the oven to 250ºF (120ºC), place the pot back in the oven uncovered, and bake for up to 3 hours.
On the flip side, if your beans seem dry after baking, try stirring them first. Sometimes, the top can look dry, but the beans are perfect underneath. If you still find your beans are dry, stir in a splash of water to loosen them.
Storage
Leftover baked beans can be stored in an airtight container in the refrigerator for up to 5 days. You can reheat them gently on the stove over low-medium heat or in the microwave. If needed, add a splash of water to loosen the sauce.
For longer storage, freeze the beans in a freezer-safe container for up to 2 months. Avoid refreezing to maintain the best texture and flavor.