Zubeidaa comes in contact with the prince of Fatehpur Vijayendra Singh (Manoj Bajpay) through her father's mistress Rose (Lillette Dubey). She falls in love with Vijayendra and becomes the second wife to the prince. The first wife is Mandakini (Rekha). Zubeidaa enters the suffocating royal world of kings and queens. Zubeidaa starts getting lonely and suffers as her husband is not able to spend time with her. Her suffering mounts again when prince takes his first wife for the campaigning of elections in the state. The over-possessive and jealous Zubeidaa takes her husband in a private plane leaving his first wife alone, but sadly the plane crashes and Zubeidaa and the prince die at young age.

The entire story of Zubeidaa is in a flashback as her grown-up son Riyaz (Rajit Kapoor) is collecting all the information about his mother through various people whom she was in contact with. The maximum help he gets is from the prince's first wife Mandakini.

The film is very sensitive and heart-touching. More than the story, it is the performances which hold you. Karisma Kapoor has grown tremendously as an actress. She plays the role of Zubeidaa to perfection. She successfully brings out every emotion and pain that Zubeidaa undergoes. She looks gorgeous. Another person who attracts attention is the ever-reliable Rekha. She plays her part with utmost conviction. Though she looks older than her role demands, she is good. Manoj Bajpay is miscast in the role of the prince. However, the supporting cast is brilliant in this film especially Surekha Sikri, Lillette Dubey and Rajit Kapoor. AR Rehman's music is good and Shyam Benegal's direction is also very good.