Preheat the Oven. Preheat your oven to 350°F. Grease a 9x13-inch baking dish with cooking spray.
Cook the Bacon and Onion. In a large skillet, cook the diced bacon over medium heat until crispy. Remove the bacon from the skillet and set aside, leaving the rendered bacon fat in the skillet. Add the chopped onion and bell pepper to the skillet with the bacon fat and cook until softened and translucent, about 5 minutes.
Prepare the Sauce. In a small bowl, whisk together the ketchup, molasses, brown sugar, Dijon mustard, apple cider vinegar, garlic powder, salt, and black pepper.
Combine the Ingredients. In the greased baking dish, combine the drained navy beans, cooked bacon, cooked onion, and prepared sauce. Stir until well combined and the beans are evenly coated with the sauce.
Bake the Beans. Cover the baking dish with aluminum foil and bake in the preheated oven for 45 minutes. Remove the foil and bake for an additional 15-20 minutes, or until the sauce is thickened and bubbly.
Serve and Enjoy. Remove the baked beans from the oven and let them cool for a few minutes before serving. Serve warm as a delicious side dish alongside grilled meats, sandwiches, or your favorite barbecue fare.