In a large Dutch oven or oven-safe pot, combine the navy beans, chopped onion, minced garlic, ketchup, water, brown sugar, ground mustard, smoked paprika, salt, and black pepper. Stir until the beans are well coated with the sauce.
Add the cut bacon to the pot, making sure it's submerged in the sauce.
Cover the pot with a lid and transfer it to the preheated oven.
Bake the beans for 8 hours, or until they're tender and the sauce has thickened.
Remove the pot from the oven and let it cool slightly before serving.