Zubeidaa is the story of Riyaz's (Rajit Kapoor) search to understand his mother, who is not known to him, as he was brought up by his grandmother in the absence of his mother. His mother's name was Zubeidaa (Karisma Kapoor) and she was the only daughter of a filmmaker named Suleman Seth (Amrish Puri). Zubeidaa acts in films secretly, but when her father finds out he forbids her to carry on and quickly arranges her marriage to Mehboob Alam. Things look happy for her when she gives birth to Riyaz. However, a misunderstanding arises between Suleman Seth and Mehboob's parents, and Mehboob divorces Zubeidaa few days after she gives birth.
Zubeidaa then meets Maharaja Vijayendra Singh of Fatehpur (Manoj Bajpai). Vijayendra is already married to Maharani Mandira Devi (Rekha) and is the father of two children. Nevertheless, he falls in love with Zubeidaa and they get married, but there is continuous turmoil in their relationship. Riyaz learns through Zubeidaa's journal that though she loved Vijayendra dearly, she was unable to follow the mainly Hindu customs and traditions of the palace, being a Muslim. She was also uncomfortable because of her brother-in-law Uday Singh's sexual advances towards her, and his demands of her to have an extra-marital affair with him. Away from her own family, she was unable to enjoy the beautiful surroundings of the palace.
Riyaz travels to Fatehpur and asks many people about his mother. However, all except Mandira, whom Zubeidaa called "Mandy Didi"' deny that his mother ever existed, or say that she was a horrible woman who seduced their king and caused his death in a mysterious accident.
On reading the journal, Riyaz finds out that Vijayendra had become a politician, and was about to go to Delhi for an important meeting. Zubeidaa felt frustrated that whenever her husband needed help he looked to Mandira for support, and at the last minute she insisted that only she will go for the meeting. They never make it, however, as they die in a plane crash. In the end, Riyaz and his grandmother watches a tape of one of his mother's films with his family. Though he loves his mother very much, Riyaz never succeeds in deciphering the mystery behind his mother's demise. It is left to the audience to decide how she died.