Step 1: Preheat your oven to 325°F (160°C). In a large, oven-safe Dutch oven or a deep, heavy-bottomed pot, cook the diced bacon over medium heat until crispy.
Step 2: Remove the cooked bacon with a slotted spoon, reserving about 2 tablespoons of bacon grease in the pot. Set the crispy bacon aside for garnish or to mix in later.
Step 3: Add the finely chopped yellow onion to the pot with the reserved bacon grease. Sauté over medium heat for 5-7 minutes, until softened and translucent.
Step 4: Stir in the minced garlic and smoked paprika. Cook for another minute until fragrant, being careful not to burn the garlic.
Step 5: Add the rinsed and drained great northern beans (or cannellini beans) to the pot. Stir to combine with the onion and garlic mixture.
Step 6: In a separate bowl, whisk together the ketchup, dark brown sugar, blackstrap molasses, apple cider vinegar, Dijon mustard, black pepper, and optional cayenne pepper.
Step 7: Pour the sauce mixture over the beans in the pot. Stir thoroughly to ensure all the beans are well coated.
Step 8: If the mixture seems too thick, add 1/2 cup of water or chicken broth. The beans should be saucy but not soupy.
Step 9: Bring the mixture to a gentle simmer on the stovetop. Once simmering, cover the Dutch oven or transfer the beans to a 9×13 inch glass baking dish and cover tightly with foil.
Step 10: Bake for 2 hours, stirring gently once or twice during the baking process to prevent sticking and ensure even cooking.
Step 11: After 2 hours, remove the foil or lid. If the beans are too liquidy, continue baking uncovered for another 15-30 minutes, or until the sauce has thickened to your desired consistency. The beans should be tender and deeply flavored.
Step 12: Remove from the oven. Let the baked beans rest for at least 15 minutes before serving. This allows the flavors to meld and the sauce to thicken further. Garnish with the reserved crispy bacon if desired.