Kunder then turned to directing. His directorial debut was titled Jaan-E-Mann. Apart from editing and composing the background music score. he also wrote the story, screenplay and dialogues. The film starred Salman Khan, Akshay Kumar and Preity Zinta, and was released on 20 October 2006. The film was a commercial failure. He then produced Tees Maar Khan his wife's 3rd directorial venture. The film was panned by critics but was declared a semi-hit at the box office.
On 9 December 2004, Kunder married director and choreographer Farah Khan, who is eight years his senior. She gave birth to their triplets, son Czar and daughters Diva and Anya, on 11 February 2008 at Mumbai's Jaslok hospital. Sajid Khan is his brother-in-law.