On the death of his first wife, he married Piari Banu Begum, daughter of Azam Khan, the second governor of Bengal during Shah Jahan's reign. She was the mother of two sons and three daughters, namely, Prince Zain-ud-din Mirza, born on 28 October 1639; Prince Zain-ul-Abidin Mirza, born on 20 December 1645; Gulrukh Banu Begum (wife of Prince Muhammad Sultan), Raushan Ara Begum and Amina Banu Begum. In 1660, she fled to Arakan with her husband, sons and daughters. Shuja was murdered in 1661. His sons were put to death. Piari Banu Begum and two of her daughters committed suicide. The remaining daughter, Amina Banu Begum, was brought to the palace, where, from grief, she died an early death. According to another source, one of Shuja's daughters was married to King Sanda Thudhamma. A year later, he scented a plot and starved all of them to death, while his wife was in an advanced stage of pregnancy by himself.