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Mr Scott and his wife, Trudy, were farewelled yesterday after a parting sermon at the church.
He has served as a pastor for 42 years, including six in Ashburton.
At 69-years-old he felt it was "just time, really".
"I’m not sure I would have thought it could be so much fun."
Mr Scott saw his time at the church through various "chapters", which included highs and lows.
The pair oversaw two major building projects at the church in 1988 and 2000.
During the latter, the congregation built more modern buildings around its 1907 base church.
Activity within the wider community was always high on his agenda as pastor, he said.
An example of this was the church’s Divorcecare programme, which gives support to people struggling with the end of their marriages.
It is something of an anomaly that its congregation doubled in those 35 years to about 300.
Although Mr Scott thought the Christian church in general was "kind of on the back foot", he did not believe this would necessarily last.
"There are still some very lively churches around and it will be interesting to see how things pan out. We have rising suicide, levels of addiction, family violence. "I wonder if in actual fact we’ll come back to the need for some spiritual values."
However, he was generally positive about Dunedin, which had a "vibrancy" now it did not in the 1980s, he said.
He was also chaplain of John McGlashan College until he quit the role four years ago.
In April, Wellington pastors Murray and Sandra Gordon will arrive to administer the church.
Mr Scott said he hoped to "stay in the community" but to give space to the new leadership.
"Mostly, my retirement will consist of cycling slowly and playing golf badly."