Preheat & Prepare: Set your oven to 350°F (175°C). Position the rack in the middle of the oven.
Render the Bacon: In a large oven-safe pot or Dutch oven over medium heat, cook the diced bacon until it becomes crispy and golden. Using a slotted spoon, transfer the cooked bacon to a paper towel-lined plate. Reserve approximately 2 tablespoons of the rendered bacon fat in the pot.
Sauté Aromatics: Add the chopped red onion and diced green pepper to the reserved bacon fat. Cook for 5-7 minutes, stirring occasionally, until the vegetables soften and begin to caramelize.
Create the Sauce: In a separate bowl, combine the tomato ketchup, dark brown sugar, blackstrap molasses, apple cider vinegar, Worcestershire sauce, and mustard powder. Whisk thoroughly until the mixture is smooth and well incorporated.
Combine Components: Add both cans of beans (with their liquid) to the pot with the sautéed vegetables. Pour the prepared sauce over the beans and stir gently to combine all ingredients.
First Baking Phase: Cover the pot with a lid and place in the preheated oven. Bake for 1 hour and 15 minutes.
Add Bacon & Continue Baking: Remove the pot from the oven and stir in three-quarters of the cooked bacon. Reserve the remaining bacon for garnish. Return the covered pot to the oven and continue baking for an additional 25-30 minutes, or until the sauce has thickened to your desired consistency.
Rest & Serve: Remove from the oven and let the beans rest uncovered for 5-10 minutes to allow the sauce to further thicken. Sprinkle with the reserved bacon pieces and sliced green onions before serving.