[1] In 1880 attention was called in the presbytery to a paper submitted by Strong titled "The Atonement" which appeared in the Victorian Review;[1] a committee appointed to investigate the article reported that some passages required explanation.

[2] The charges appeared to some to have been tenuous, one of his principal accusers said of one passage that "the words were perfectly harmless in themselves but conveyed an impression of unsoundness to his mind".

What might have passed in Scotland without great upheaval was likely to take a different turn in Victoria, whose Presbyterian Assembly was chaired by hard-line fundamentalist Moderator John Gardner.

With continuing friction in the presbytery, Strong tendered his resignation on 8 August 1881; however he agreed to take six months leave instead at the request of church officers and the congregation.

[1] Strong left his family in Melbourne and visited Scotland from March to October 1882 after a speech by a Scots Church elder, J. C. Stewart, reignited attacks on him.

[1] On Strong's return to Melbourne he was admonished by the presbytery for supporting the opening of the Public Library and Art Gallery on Sundays.

On 14 November 1883 a large number of his friends met at the Melbourne Town Hall to express their sympathy with Strong and to present him with a cheque for £3000[1] (at least $500,000 in today's values).

[4] and disavow all complicity with the doctrines of the lecture and declare his faith in the true deity of the Lord Jesus Christ, the propitiatory character of his death and the real resurrection of his body from the dead.

[5] For various reasons, including difficulties with his assistants, the economic situation and Strong's sympathy for the manual workers, the richer members of his congregation dropped away and in 1922 a smaller church was built in Russell Street.

From 1887 until his death Strong edited a monthly periodical known variously as Our Good Words (1887–89), The Australian Herald (1889–1908) and The Commonweal (1908–42).