Preheat your oven to 325°F (163°C) with the rack in the lower third. A fully preheated oven ensures even baking.
In a large Dutch oven over medium heat, cook the bacon pieces until golden and crispy around the edges, about 6 to 8 minutes. Transfer bacon to a paper towel-lined plate, leaving the rendered fat in the pot.
Add the diced onion to the pot and cook in the bacon fat until soft and translucent, 5 to 7 minutes. Add the minced garlic and cook for 60 seconds until fragrant, stirring constantly to prevent burning.
Reduce heat to medium-low and add the molasses, brown sugar, ketchup, apple cider vinegar, and Worcestershire sauce. Stir well, scraping up caramelized bits from the bottom. Add the dry mustard, smoked paprika, garlic powder, salt, and pepper, stirring until combined and bubbling gently, about 2 minutes.
Add both cans of drained navy beans to the sauce and stir gently to coat every bean evenly. Pour in 1/4 cup (60ml) of reserved bean liquid or water to loosen the mixture slightly.
Stir about two-thirds of the cooked bacon pieces back into the bean mixture. Reserve the remaining one-third to scatter over the top before baking.
Cover the Dutch oven with its lid (or transfer to a 9x13-inch baking dish and cover with foil). Bake at 325°F (163°C) for 30 minutes. Carefully remove the cover, scatter the reserved bacon over the top, and bake uncovered for another 25 to 30 minutes until bubbling and slightly thickened.
Remove from the oven and let rest uncovered for 5 to 10 minutes to allow the sauce to thicken. Taste and adjust salt and pepper if needed before serving warm.