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.
Drain and rinse the beans with cool water. Place the drained beans back in the pot and cover them with 6 cups (1 ½ L) of fresh cold water. Bring the beans to a boil over medium-high heat. Once boiling add the baking soda. Reduce the heat, place the lid on the pot, and simmer the beans for 30 minutes or until tender.
Preheat the oven to 250ºF (120ºC).
Drain the cooked beans into a colander fitted over a large bowl or other 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 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. Stir to mix. Add the 3 ½ cups of reserved bean liquid and the beans to the pot. Stir well to combine.
Place the lid on the Dutch oven and place the beans in 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
I use raw bacon and raw onion and mix them straight into the pot of beans with the other ingredients. You could lightly cook the bacon and onion together beforehand if you want, however, it's not necessary.The main reason to add baking soda to beans while they boil is to help them soften faster during the cooking process (I've also read baking soda will help reduce flatulence after eating, so that’s a good reason too).If your beans are watery when you take them out of the oven after baking don’t fret! They will thicken as they cool. If for some reason your beans don’t thicken, preheat the oven to 250ºF (120ºC), place the pot back in the oven uncovered, and bake for 1 hour.To store, scoop cooled beans into plastic or glass container with lids and keep in the fridge for up to one week.Molasses baked beans freeze exceptionally well! Once cool, store them in airtight containers with tight fitting lids. They will keep in the freezer for up to three months.To reheat frozen beans, thaw molasses baked beans in the fridge for 24 hours, or on the counter for a few hours, then heat gently in a pot or in the microwave.
Substitutions
I made this recipe with yellow eye beans for years, and they're great, however, I now use dried white navy beans. Navy beans have a creamier texture after baking which I prefer.Regular smoked, or double-smoked bacon, is my go-to for molasses baked beans, however, salt pork is also a good substitute. If using salt pork, consider adding a teaspoon or two of liquid smoke before baking to get more of a smoky flavour.I tried making molasses baked beans in my slow cooker once, and they were ok, however, my slow-cooker beans turned out quite watery. I had to cook them a few hours longer than this oven-baked version.Make this recipe plant-based! Just substitute 1 to 2 teaspoons of liquid smoke for the bacon and continue to follow the recipe and cooking times exactly as written.I haven’t tried it myself, however, I think maple syrup could be a safe bet to swap for molasses at a 1:1 ratio. Because maple syrup is less thick than molasses, you may need to bake your beans a bit longer. Other sweetener options if you don't have molasses or maple syrup could be to double the brown sugar, or try a mix of brown sugar and applesauce. Again, I haven't tried these options but I think they could work.