Rev John MacFarlane had been Minister of the Martyrs Church Paisley for 3 years, when he was chosen to accompany the 150 Scottish immigrants on the 'Bengal Merchant' leaving the Clyde on 31 October 1839. They arrived at Port Nicholson on 20 February 1840, and on the following Sunday (23 February) he conducted his first service on Petone beach. There was a Southerly blowing & rain falling, making it muddy under foot, but they sang hymns & worshipped in the open on their first Sunday in their new country. This spot is now marked by a Celtic Cross. Thereafter he held service every Sunday in Bethune's store on the Hutt River.
"For some time after his arrival, he ministered to the needs of every Protestant in the community, tramping long miles in his plaidie and preaching in English or Gaelic according to the needs of his congregation."
When the settlement moved to Thorndon, services were held first in Hunter's premises, and later in the Exchange, Customhouse Quay. He also preached in the native chapel at Te Aro, and in the Courthouse Thorndon. He preached in Gaelic at Kaiwarra for the Highland settlers, the first Gaelic sermon being preached on 20 June 1844. For some weeks, until the arrival of the first Anglican clergyman, Rev John Macfarlane ministered to the needs of all Protestant colonists. As a result of a visit to Nelson in 1842 he appealed to the Colonial Committee of the Church of Scotland for a Minister for the Nelson district.
The draft constitution of the first Presbyterian Church in Wellington was drawn up and unanimously approved in March 1843; it was a parish of the Church of Scotland and not a part of the Wellington Presbytery when it was formed, nor had it any formal relation to the PCNZ until 1874; the congregation and Minister petitioned the 1874 General Assembly to be received into the PCNZ, which was cordially agreed to.
In April 1843 the Rev James Duncan arrived as Missionary to the Maoris in the Manawatu. He made his headquarters in Wellington while studying the Maori language, and assisted the Rev Macfarlane.
He officiated at the opening of the new Church (St Andrews) on 17 January 1844 Rev Macfarlane left for a visit "only a visit" to Scotland by the 'Bella Marina' in October 1844 and the Church was closed during his absence. He intended to be absent only 18 months, but owing to the state of his health he was unable to return to New Zealand but settled as Minister of Lochgilphead, where he was inducted on 7th September 1847. He married in 1852 and died in March 1859 at Lochgilphead and was buried in the churchyard of the parish church.