Annie Jane Allen was born probably on 22 November 1835 and baptised at Leamington Priors, Warwickshire, England, on 25 December 1835. She was the daughter of Elizabeth Dodd and Edward Allen, a businessman and farmer. Little is known of her early life. The Allens arrived in New Zealand on the Black Eagle in 1861 and settled at Mount Albert in Auckland.
Soon afterwards, the devoutly religious Annie Allen was asked by ex-missionary Eliza White to teach at the Wesleyan mission school at Kāwhia on the west coast of the North Island. She agreed and went to the mission in November 1861. The arduous journey took a fortnight. She travelled by bullock dray to Mercer, by Māori canoe up the Waikato and Waipā rivers, on foot to the head of the Kāwhia Harbour and then by canoe again to the mission station. At Kāwhia she worked with Cort Henry Schnackenberg, a Wesleyan minister. After his wife's death in 1863, he and Annie were married in Auckland on 12 May 1864. Schnackenberg, born in the German kingdom of Hanover, had come to New Zealand in the early 1840s via England and Australia. The couple were to have three daughters and two sons.
As well as dedicating herself to being a housewife, Annie Schnackenberg assisted her husband with mission duties. These included preaching at services, writing letters – particularly official communications with the government – and keeping the mission's accounts. Because the mission was expected to be self-sufficient, she grew fruit and vegetables and taught her female pupils how to sew their own clothes.
Church authorities considered it too dangerous for the Schnackenbergs to continue living at the Kāwhia mission on the edge of the King Country because of a Kingite embargo on Pākehā travelling into that region. They were transferred to Raglan. The Schnackenbergs had good relations with Māori; it is said that theirs was the first Pākehā house that King Tāwhiao visited once fighting had ended in Waikato in 1864.
On 10 August 1880 Cort Schnackenberg died and Annie returned with their children to her parents' house in Auckland. She divided her time between church and Sunday school work at the Mount Albert Methodist Church, and became involved with Christian women's organisations. By 1882 she was a church leader at the Pitt Street Wesleyan Church.
Annie Schnackenberg was a founder member of the New Zealand Women's Christian Temperance Union, established in 1885. She was national president from 1891 to 1901 and became vice president-at-large in 1901. She was president of the Auckland branch of the union from 1889 to 1897. As one of the earliest advocates of temperance instruction in schools, she became superintendent of the scientific temperance instruction department. During her term in office temperance textbooks were ordered by the Department of Education, making it possible, subject to the approval of headmasters and local school committees, for temperance to be taught in New Zealand schools.
The WCTU was at the forefront of the agitation for women's suffrage in New Zealand, and it was during Schnackenberg's time as national president that women in this country were granted the vote. Schnackenberg thought that this achievement was just as important as the temperance aspect of the WCTU's work. In 1893 she publicly thanked God for the enfranchisement of women and suggested that members should try to influence other women to make the best use of the rights they had gained. In her opinion the vote was 'a sacred trust to be used for the advancement of every righteous cause.' However, her view of the future was not radical; she felt that universal suffrage alone was sufficient to ensure the equality of women and men and did not believe that women wanted to become members of Parliament.
Other WCTU reforms supported by Schnackenberg included the raising to 21 of the age of consent for girls and the repeal of the Contagious Diseases Act 1869, which made legal the compulsory examination of prostitutes (but not their clients) or women thought to be prostitutes. Any act of Parliament, she felt, which 'interferes with the rights and liberties of women only to make it safe for men to sin, is a disgrace to a community calling itself Christian'. Schnackenberg represented the WCTU at the inaugural meeting of the National Council of Women of New Zealand in Christchurch in 1896, where she was appointed a vice president. Her attendance at the annual sessions was not regular, but when present she spoke strongly in supporting the repeal of the Contagious Diseases Act.
Because of her fluency in Māori, gained during her time as a teacher at the mission schools in Kāwhia and Raglan, she was appointed superintendent of Māori work. The union was disturbed at evidence of alcohol abuse among Māori and placed great emphasis on proselytising Māori women. Schnackenberg travelled to settlements such as Ōhinemutu and Whakarewarewa in the central North Island to advocate temperance and the observation of the sabbath.
Annie Schnackenberg was also a member of the YWCA, founded in Auckland in 1885. While on the board from 1890 to 1903, she worked on a social committee organising entertainment for the girls at the YWCA rooms and served as acting president (with Susie Mactier) from 1899 to 1901. Ill health prompted Annie Schnackenberg to give up the presidency of the WCTU in 1901. Serious illness in 1903 curtailed her involvement with the YWCA and she was an invalid for two years before her death in Auckland on 2 May 1905. She was remembered for her 'warm-hearted sincerity, unfailing good nature' and 'remarkable gift of common sense.'