In an oven-safe dish, whisk together the molasses, brown sugar, ketchup, yellow mustard, onion powder, baking soda, smoked paprika, and kosher salt until smooth.
Stir in the drained and rinsed navy beans until evenly coated with the sauce.
Bake in the preheated oven for 20-25 minutes. Stir halfway through to help the sauce thicken and the flavors meld.