Brown bacon, onion and green pepper in a large saucepan over medium heat until bacon fat renders and the onions are transparent and golden.
Add all the other ingredients except the salt, pepper and jalapeños. Gently simmer until the beans are richly flavored, 30 minutes, adding small amounts of water as needed to prevent burning. Taste and add salt and pepper as desired. Add jalapeños during the final minutes of cooking.
For true baked beans, simmer the mixture for five minutes and transfer to a 13-by-9-inch aluminum foil pan or casserole dish. Bake uncovered in a 350 degrees oven for 30 minutes or until bubbly. Stir in jalapeños just before serving.
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