Baigent was born in March 1948 in Christchurch, New Zealand. He grew up in Motueka and Wakefield, small communities on the sparsely-populated South Island of New Zealand. His upbringing was Catholic, and he attended church three times a week, as well as being tutored in Catholic theology from the age of 5. His father left the family when he was 8 years old, and Baigent took the name of his maternal grandfather, Lewis Baigent. His great-grandfather had founded a forestry firm, "H. Baigent and Sons".
His secondary schooling was at Nelson College, and then he moved on to Canterbury University, Christchurch, initially intending to study science and continue in the family career of forestry, but then switched to studying comparative religion and philosophy, studying Buddhism, Hinduism and Christianity. He traveled to Australia and Southeast Asia, occasionally living on the street. He then returned to Auckland, receiving a BA in Psychology.
Michael Baigent worked briefly at the BBC photographic department, and worked night shifts at a soft-drink factory. Later in life, Baigent earned an MA in Mysticism and Religious Experience at the University of Kent.
A Freemason and a Grand Officer of the United Grand Lodge of England, he has been editor of Freemasonry Today since April 2001, which he has used as a platform for a more liberal approach to Freemasonry. He is a trustee of the Canonbury Masonic Research Centre.
He currently lives in Bath with his wife, Jane. They have two daughters.