Heat the olive oil in a medium saucepan. Add the onion, garlic, salt, black pepper, chipotle pepper flakes, and ground cumin. Cook the mixture for 6 to 8 minutes, or until the onions are translucent and soft.
Add the brown sugar, ketchup, apple juice, vinegar, and mustard. Bring the mixture to a boil, reduce to a simmer, and cook for 20 minutes longer.
Remove from the heat and set aside to cool. Use the sauce immediately or cover and refrigerate, for up to 2 weeks, until ready to use.