In a blender or food processor, combine the chopped onion, orange juice, lime juice, apple cider vinegar, vegetable oil, annatto paste, dried oregano, ground cumin, ground cinnamon, ground allspice, salt, and minced garlic. Blend until smooth. Cut the young jackfruit into pieces that resemble shredded pork.
In a large bowl, combine the jackfruit and the marinade. Mix well to coat the jackfruit.
Cover the bowl with plastic wrap and refrigerate for at least 2 hours or overnight to allow the flavors to meld.
Preheat the oven to 325°F (160°C).
Transfer the marinated jackfruit to a Dutch oven or baking dish with a lid. Cover the dish tightly with aluminum foil.
Bake for 3-4 hours, until the jackfruit is tender and has absorbed most of the liquid.
Remove the dish from the oven and use a fork or potato masher to shred the jackfruit.
Serve the vegan Cochinita Pibil with corn tortillas and your favorite toppings, such as chopped cilantro, diced onion, avocado, and lime wedges.