John McIndoe was born at Rothesay, on the isle of Bute, Scotland, on 29 November 1858. He was the son of Elizabeth Gillies and her husband, James McIndoe, a grain merchant. Both the McIndoe and Gillies families had connections with New Zealand. James McIndoe had been a member of the Otago Association (as had his father), and Elizabeth McIndoe's father, John Gillies, and most of the rest of her family had by this time already emigrated to Otago.
Brought by his parents to Dunedin in 1859 on the Alpine, John was educated at Caversham School. On 1 January 1874 he was apprenticed as a compositor for the usual five years to Coulls and Culling, printers of Dunedin. Apart from periods in Sydney and Christchurch he spent most of the 1880s in Dunedin, working as a compositor for the printers and stationers Fergusson and Mitchell. The superior quality of his workmanship was highly praised. That most discerning judge, the typographer and printer R. Coupland Harding, in 1890 described McIndoe's work for Fergusson and Mitchell as 'some of the best typographical designing that we have seen done in New Zealand'. Later examples of his printing show a restrained elegance in advance of the prevailing late nineteenth century taste for ornament.
McIndoe's capacity to succeed at a time when the struggle for commercial survival was particularly keen is shown by his subsequent career. From 1893 to 1900 he was in partnership as a printer with David Cherrie, trading as Cherrie and McIndoe from premises in Jetty Street. In August 1900 McIndoe set up on his own as John McIndoe, Printer and Bookbinder, soon moving to new premises in Vogel Street. The business of jobbing printing and bookbinding was profitable, if not greatly so, and grew steadily. For many years the Dunedin City Corporation was a major client. The firm of John McIndoe built up a reputation for artistic and creative printing.
From 1879 John McIndoe served in the volunteers. As captain and quartermaster of the 1st Battalion of the Otago Rifle Volunteers he was involved in the equipping of contingents to the South African war (1899–1902). A Presbyterian by upbringing, he became a prominent Freemason, serving for many years as district grand secretary of the Otago and Southland lodge. For some years he was a committee member and chairman of the Macandrew Road School Committee. He was also for some time honorary treasurer of the Otago Art Society.
On 12 January 1898 at Wellington John McIndoe married Mabel Hill, a singer and artist, and sister of the composer Alfred Hill. They were to have four children. Mabel Hill had been an art instructor at Wellington Technical School, and had studied with the painter James Nairn. She continued to paint and exhibit her work after her marriage, and was active in the Otago Art Society.
Illness forced John McIndoe to retire prematurely, and he died at Seacliff, near Dunedin, on 4 April 1916. His firm continued under his son, John Leslie McIndoe, and later his grandson, John Hector McIndoe, under whom it became noted as a book publisher. From 1945 Mabel McIndoe lived in England, near one of her sons, the plastic surgeon Archibald McIndoe. She continued to paint until the end of her life, and died at East Grinstead, Sussex, in 1956.