On 8 May 1963, which also happened to be the date of that year's Kaamatan festival, he married Datin Nancy Mary Mobijohn (26 May 1945 – 13 October 2023), who was the daughter of a local politician and a former teacher-cum-colleague of his named Datuk Seri Panglima Lidwin Anthony Mobijohn (1921 – 2002) and wife, Datin Seri Panglima Nora Joguim Sipanil (1923 – 2008), also hailing from the same village and the couple had five children, three boys and two girls, including Donald Peter Mojuntin (born 26 January 1965) and Deidre Peter Mojuntin (28 December 1973 – 1 January 2003), the winner of the Unduk Ngadau pageant in 1989.

The smell of blood was terrible and my chaps were at the point of fainting, but we managed to get the bodies out of the plane and lined up near to it so that we could make a quick identification.

[1] The location of the crash is commemorated with the Double Six Monument, a memorial marked with a stone obelisk that was erected shortly after the accident.

His remains now rests at the cemetery of St. Michael's Church, Penampang with his wife, Datin Nancy Mary Mobijohn[3] by his side, who passed away at the age of 78 on 13 October 2023.

Since many Sabahans at the time live in isolated up river kampongs and remote hill villages, he would travel days and nights with minimum rest.

Mojuntin went through the Kinabatangan river by raft to visit the Rungus and Orang Sungai villages of the deep interior to ask for their thoughts and educate them on situations that are happening in Sabah.

The unwanted expulsion of missionaries and church personnel, which made way for the course of Islamisation and anti-Christian sentiment in Sabah was strongly criticised by him, for he was a loyal devout Catholic.

Dubbed as the Golden Son of the Kadazan, Mojuntin's position is documented in the published biography of Bernard Sta Maria and for the alleged defamation of the then-Chief Minister of Sabah, Tun Mustapha, the book was banned by the Malaysian Home Ministry in June 1978.

However, throughout the years, multiple groups and non-governmental organisations (NGOs) have voiced out that the ban on the book should be lifted as it contains the history of Sabah before, during and after becoming part of the Federation of Malaysia, including Tan Sri Lim Kit Siang.

In June 2024, chairman of the Sunduvan Sabah non-governmental organisation (NGO), Aloysius Danim Siap said, the group wants the younger generation to learn how the Double Six crash changed the state's political landscape.

[9] Mojuntin's granddaughter, Atalia Mae Albert Jaua, has taken a stand against the book's ban as well, writing an open letter to Prime Minister Datuk Seri Anwar Ibrahim, calling for its removal.