If your chipotle peppers are whole, finely mince them or briefly pulse them in a food processor until they form a smooth paste.
In a medium saucepan, whisk together the ketchup, minced chipotles in adobo, apple cider vinegar, dark brown sugar, molasses, and Worcestershire sauce.
Stir in the garlic powder, onion powder, cumin, black pepper, and salt until all the spices are fully incorporated.
Place the saucepan over medium heat and bring the mixture to a gentle simmer, whisking frequently to prevent the sugars from sticking.
Reduce the heat to low and let the sauce bubble gently for 15 minutes. This allows the smoky capsaicin from the chipotles to infuse completely into the sweet tomato base.
Remove from the heat and let the sauce cool entirely. Transfer to an airtight jar and store in the refrigerator for up to 2 weeks!