Dunston Checks In is about a lovable orangutan named Dunston and his jewel-thief master, Lord Rutledge, and the shenanigans they get into when they check-in to a posh Manhattan hotel. Robert Grant is the manager of The Majestic Hotel, which is a five-star luxurious establishment, and he is dedicated to keeping his guests happy. When the hotel's owner, Mrs. Dubrow, tells Grant that an undercover reviewer from the La Monde Traveler Organization is coming to the hotel, he has to keep the hotel and its staff sharp. If they do well, the hotel receives the prestigious Sixth Star award and Grant could receive a promotion as well. However, Grant finds that nothing is ever as easy as it sounds.
Lord Rutledge intends to steal the guests' jewelry with Dunston's help. Dunston, tired of living the life of crime and being treated poorly by his owner, escapes with the help of Grant's sons, Brian and Kyle. Meanwhile, Mrs. Dubrow mistakenly believes that Lord Rutledge is the undercover reviewer and treats him with kid gloves.
Brian and Kyle try to keep Dunston hidden from their father and Dunston's evil owner, but Grant eventually encounters Dunston. Grant calls in the Animal Control Unit to capture the orangutan. When Brian and Kyle try to convince their dad that Dunston is not a nuisance and reveal Lord Rutledge's true intentions, Grant decides to stand up to the hotel's owner. However, Mrs. Dubrow fires Grant. After being humiliated by Dunston's antics, the real critic is revealed and decides not to award the Sixth Star to the Majestic. Lord Rutledge is arrested and Mrs. Dubrow has to apologize to Grant and his sons.
This heartwarming movie ends when Grant accepts a new job opportunity with the hotel's empire and moves his family to Bali. His sons are delighted to learn they can keep Dunston as a pet.