Sort through the navy beans to remove any debris or discolored beans, then rinse them thoroughly under cold water. Place the cleaned beans in a large pot and cover with 6 cups of water. Bring to a boil over high heat, then add the baking soda—this helps soften the beans and reduces cooking time. Cover the pot and reduce heat to maintain a gentle simmer for 30 minutes. The baking soda will create some foam, which is normal. After simmering, drain the beans in a colander and reserve 3½ cups of the cooking liquid (this starchy liquid helps create the sauce). Rinse the beans briefly under cool water and set aside.

While the beans simmer, cut the bacon into 1-inch pieces and cook in a large skillet over medium-high heat until crispy, about 8-10 minutes. Remove the bacon with a slotted spoon and set aside, leaving about 2 tablespoons of bacon fat in the pan. Add the finely diced onion to the same skillet and sauté in the bacon fat for 3-4 minutes, stirring occasionally, until softened and slightly translucent. This builds a flavorful base for the beans. I prefer to cook the bacon and onion together this way because the bacon fat adds incredible depth to the vegetables.

Preheat your oven to 250°F. In a large pot or Dutch oven, combine the ketchup, molasses, cider vinegar, brown sugar, mustard powder, ground black pepper, smoked paprika, and kosher salt. Stir well until all the dry spices are fully incorporated and the mixture is smooth. This sauce base is where all the flavor lives—the molasses and ketchup create richness, the vinegar adds brightness, and the spices bring complexity. Take a moment to taste the sauce base with a spoon to ensure the flavors are balanced before adding the beans.

Add the parboiled beans from Step 1, the reserved 3½ cups of bean cooking liquid, the cooked bacon and onions from Step 2, and the sauce base from Step 3 into the pot or Dutch oven. Stir everything together gently but thoroughly, ensuring the beans are evenly coated with the sauce and the liquid is well distributed. Cover the pot with a lid (aluminum foil works if you don't have one) and place it in the preheated 250°F oven. Bake for 8 hours, stirring occasionally—I recommend checking and stirring every 2 hours to prevent sticking and ensure even cooking. I like to keep the beans slightly soupy after 8 hours; if they look too dry at any point, add a bit more water to maintain a nice consistency.

After 8 hours of baking, remove the beans from the oven and stir well. The beans should be very tender, and the sauce should be thick, rich, and coating each bean. Taste and adjust seasoning if needed—you can add a pinch more salt or a splash of vinegar for brightness if desired. Let the beans rest for 5-10 minutes before serving, which allows the flavors to meld and the sauce to set slightly. Serve warm as a side dish with grilled meats, cornbread, or however you prefer.