The relationship between Saif Ali Khan and his former wife, Amrita Singh, continues to be a subject of public interest, particularly regarding their children, Sara Ali Khan and Ibrahim Ali Khan. Saif Ali Khan has stated that Amrita Singh was never compelled to convert to Islam, and that their differing religious beliefs were respected throughout their marriage.

Amrita Singh, who was raised Sikh, reportedly converted to Islam before marrying Saif Ali Khan in 1991. They had an Islamic wedding. Saif, the son of the late Mansoor Ali Khan Pataudi and actress Sharmila Tagore, comes from the royal Pataudi family. Sharmila Tagore converted to Islam after marrying Mansoor Ali Khan Pataudi.

Saif Ali Khan emphasized that he and Amrita Singh followed the principle of "To each his own religion" from the beginning of their relationship. He recounted instances where Amrita Singh would visit the Gurudwara (Sikh temple) for prayers, and he would stay home to babysit their children, Sara and Ibrahim. He trusted that Amrita would not influence the children in any way regarding religion.

The couple eventually divorced in 2004. Saif expressed concern for Sara and Ibrahim, who were in Amrita's custody after the separation. Saif and Amrita's children are often seen visiting religious places with their mother. For example, Sara Ali Khan and Amrita Singh have been spotted together at the Ajmer Sharif Dargah. In January 2025, Sara and Ibrahim were seen visiting their father, Saif Ali Khan, at Lilavati Hospital after he was injured during a home intrusion.

Despite their divorce, both Saif and Amrita have seemingly maintained a cordial relationship for the sake of their children. Sara Ali Khan has spoken publicly about her parents' separation, stating that it was the right decision for their happiness. She emphasized that everyone is happier as a result. Saif Ali Khan married Kareena Kapoor in 2012, and they have two sons, Taimur and Jeh. Sara and Ibrahim are often seen spending time with their father and his family.

Saif Ali Khan's upbringing also involved exposure to different faiths. His mother is Hindu, and his father was Muslim. He grew up in a Muslim atmosphere, and his grandmother played a central role in his religious education. He attended chapel while studying in England, but later chose not to, identifying as Muslim.