John Alexander Wilson was born probably on 21 April 1829 at Condé-sur-Noireau, Calvados, France, the eldest son of John Alexander Wilson, a naval officer, and his first wife, Anne Catherine Hawker. In 1832 his father was accepted as a lay preacher with the Church Missionary Society. The family sailed from London on 21 September 1832 on the convict ship Camden to Port Jackson, New South Wales, Australia. They continued on the Byron to the Bay of Islands, New Zealand, arriving on 11 April 1833. Anne Wilson died at Te Papa mission station, Tauranga, on 23 November 1838, leaving her four young sons to be brought up by their father.
John was educated at the CMS school at Waimate North, King's School, Parramatta, New South Wales and St John's College, Auckland. He began farming in 1845 at Ōpōtiki with his brother Charles and from 1852 farmed in East Tāmaki. He married Anne Lydia Dent on 20 November 1855 at St Helier, Jersey, in the Channel Islands, and the first of their 12 children, also named John Alexander, was born there in 1856.
Having returned to New Zealand, on 7 October 1857 Wilson was elected to the Auckland Provincial Council for the Pensioner Settlements electorate. On the outbreak of war in Waikato in July 1863 he enrolled in the Auckland Militia and was present at the ambush at Williamson's Clearing on 25 August 1863, an action which subsequently entitled him to receive the New Zealand Medal. At his own expense he raised No 2 Company of the 3rd Regiment, Waikato Militia, serving as captain until his resignation in 1864. In 1865 he was appointed captain of the 3rd Battalion of the Auckland Militia, only being placed on the Retired List in 1907.
After the wars of the 1860s Wilson was employed in government positions over a period of 35 years. Much of his service was in the Bay of Plenty, East Coast and Poverty Bay areas, where he was special commissioner for settlement of Bay of Plenty confiscated land from 1866 to 1868, and land purchase officer for the East Coast and Bay of Plenty district from 1873 to 1876. His criticism of Judge John Rogan and the workings of the Native Land Court on the East Coast, first published as a series of letters to the Otago Daily Times and subsequently republished in pamphlet form, led to his dismissal from the position of land purchase officer in 1876.
Despite this he was appointed a judge of the Native Land Court in 1878, a position that was terminated in 1880. Wilson claimed in a pamphlet published in 1884 that his dismissal was due to false representations and the animosity of the chief judge. The judge in question was F. D. Fenton, who dismissed Wilson on the grounds that he had no legal training. There had been conflict over Wilson's ability to devote enough time to his court obligations while he held other government positions. He had also remained in Tauranga while Fenton insisted that judges base themselves in Auckland and move around the circuit. Wilson was reappointed in 1886 and served until 1891, and again from 1895 to 1901. He dealt with nearly two million acres of Māori land.
Wilson was intelligent, ambitious, and enterprising, but also self-centred, and intolerant. His contemporary, Gilbert Mair, described him as 'far from being a humorous man'. At the time of his dismissal in 1876 he was regarded as zealous and hard-working, but it was deemed necessary to remove him from office because he could not get on with other officers in the district. Nor was he able to get along with the people of Tauranga.
In 1874 Wilson, in partnership with William Kelly, had purchased the volcanic White Island (Whakaari) from George Simpkins. In 1878 he bought land in Tauranga on which to build a sulfur works and acquired a 43-foot cutter, the Tāmaki Packet. He began to export White Island sulfur to Australia. By 1880 the works, managed by Wilson's son, Charles Hawker Wilson, was processing the sulfur. John Wilson visited Melbourne in 1881 in an attempt to raise £30,000 capital to expand the plant. Failing in this he decided to float the company locally. Although the proposition received active support from the Bay of Plenty Times, there was considerable local opposition.
Nevertheless, the New Zealand Manure and Chemical Company was formed in 1883, with a capital of only £2,400. The company took over the sulfur works but retained John Wilson, who received 2,000 £1 shares free of charge, as managing director. The first sulfuric acid and superphosphate were manufactured in 1884. At the official opening of the expanded plant on 14 October 1884, Wilson claimed that no one had ever contemplated using an active volcano for trade purposes before.
However, handicapped by the depression and an unrealistic contract with Wilson the company failed to prosper. Wilson's directors complained that they found great difficulty in acting cordially with him, and he showed he did not trust them. Refusing to compromise, Wilson resigned, and the company went into liquidation in 1886. The shareholders, mostly leading citizens of the Tauranga district, suffered great losses.
Wilson continued to work the White Island sulfur deposits, but refused to let Tauranga people land on the island. A town meeting was held at which it was resolved to send a letter to the minister of justice censuring Wilson's behaviour. A bonfire was built on the beach, on which his effigy was burned, and sulfur stored in a shed on the mainland was set alight on several occasions. Wilson retained his share of White Island until about 1901, when he sold it to the New Zealand Loan and Mercantile Agency Company.
In addition to his two polemical pamphlets Wilson published a cosmological and climatological treatise, The immortality of the universe (1875), and two works of Māori history. He was in close contact with Māori for much of his life: in his early years in the mission stations, in his war service, and in his land court work. The story of Te Waharoa (1866) is an outline of events in the life of the Ngati Haua leader, and Sketches of ancient Māori life and history (1894) is a brief account of pre-European Māori life, reprinting articles he had contributed to the Auckland Star.
Wilson died in Auckland on 28 April 1909. Anne Wilson died there on 20 February 1915.