Preheat the oven to 350 degrees F (175 degrees C).
Heat oil in a large skillet over medium-high heat. Add onion and jalapeno. Cook until onion is soft and translucent, about 5 minutes. Add garlic and cook for 1 minute. Add bourbon and simmer for 4 minutes. Turn heat off.
Combine tomato paste, maple syrup, molasses, vinegar, soy sauce, mustard, and paprika in a large bowl; whisk until smooth. Add onion mixture and beans; gently stir to combine.
Transfer to a baking dish. Cover and cook for 35 minutes. Uncover and cook for 15 more minutes. Remove from the oven and let sit for 5 minutes before serving.