Blu and Jewel are relishing their life in Rio with their trio of children: the eldest, Carla, who is passionate about music; the intellectually curious Bia; and the playful youngest, Tiago. Concurrently, Blu's former owner, Linda Gunderson, along with her husband, Tulio, an ornithologist, embarks on an exciting expedition in the Amazon, where they stumble upon a rapid-flying Spix's macaw that has unfortunately lost a feather. Upon hearing about this discovery through the news, Jewel feels a strong urge to venture into the Amazon in search of the blue macaws, believing it’s crucial for Blu, who has yet to experience what it is like to be with his own kind. Despite her enthusiasm and the kids' excitement, Blu is hesitant but ultimately feels compelled to join the adventure.
Their friends, Rafael, Nico, and Pedro, opt to accompany them, while Luiz tries to join but is left behind. In preparation, Blu packs a fanny pack filled with supplies, prominently featuring a GPS device, which Jewel finds quite annoying.
Meanwhile, a notorious illegal logging leader known as Big Boss becomes aware of Linda and Tulio's mission and sends his henchmen to eliminate any potential interruptions to their destructive plans. Adding to the chaos, Blu and Jewel's archenemy, Nigel, the cockatoo who survived the crash from their previous adventure, is now grounded but devises a plot for revenge, employing two sidekicks: a mute anteater named Charlie and a love-struck poison dart frog named Gabi.
As Blu and his family travel by boat toward the jungle, Nigel prepares to strike back during their journey; however, his plans are foiled when Charlie unintentionally triggers the emergency horn, awakening everyone on board. Upon reaching the jungle, they initially find nothing, but not for long, as they discover a secret paradise where a flock of blue macaws resides. There, they meet Jewel's strict long-lost father, Eduardo, her elder sister Mimi, and her childhood friend Roberto. Eduardo, however, disapproves of Blu's domestic demeanor.
While searching for the blue macaws, Linda and Tulio find themselves ensnared by the loggers. Simultaneously, Blu endeavors to integrate himself into the flock despite their aversion to humans. He pleads with Eduardo to reach out to Linda, asserting that she could save their entire group, but Eduardo strictly forbids any contact with humans and warns Blu of the dangers.
During a training session aimed at helping Blu adopt the flock’s survival techniques, things don't go smoothly. Meanwhile, Nigel, in disguise, aims to eliminate Blu during a vibrant Carnival audition hosted by Rafael, Nico, Pedro, and Carla. In a humorous yet disastrous turn, Blu inadvertently sparks a conflict between the Spix macaws and their fierce enemies, the Scarlet macaws, led by the aggressive Felipe, when he accidentally strikes Felipe with a twig during a Brazilian nut gathering. This misstep ignites a full-blown food war reminiscent of a soccer match, where Blu clumsily costs his new family their resources when he accidentally sends the fruit into their own goal.
After discovering the destruction left in the wake of the loggers, Blu resolves to help Linda and Tulio while sending Roberto to alert the flock of the impending threat. Blu rallies the blue macaws to defend their habitat, joining forces with the Scarlet macaws and other jungle animals to overpower the loggers. In a last-ditch effort, Big Boss attempts to demolish the trees but is thwarted when Blu snatches the lit dynamite.
In a climactic showdown, Blu and Nigel find themselves entangled in vines as their battle unfolds. Gabi and Charlie unwittingly assist by shooting Blu with a dart, only for it to hit Nigel instead, resulting in a dramatic and theatrical death speech from Nigel as he appears to succumb to fate. Gabi, believing in her own poisoned state, attempts to end her life — only for Bia to reveal that Gabi's toxicity was a myth. As Nigel makes one final attempt on Blu's life, he finds himself overwhelmed by Gabi's affections.
With the loggers defeated and the flock now safely under Linda and Tulio's guardianship, Blu and Jewel choose to settle in the Amazon alongside their family and friends, while still promising to return to Rio during the summer. As the journey concludes, Nigel and Gabi are escorted back to Rio by Tulio, Luiz finally makes it to the Amazon after hitching a ride with Kipo, and Charlie becomes a new member of their avian assembly, concluding a wild adventure filled with family, danger, and unexpected friendships.
