As part of the project, which is expected to cost more than $100,000, the sprinkler system will be extended, the ceiling cleaned, stained-glass windows repaired and the organ will undergo maintenance.
The scaffolding, which stood 20m high in places, was put up over a four-week period by Bramwell Scaffolding contractors.
One thousand planks were used on the framework. .
"It was a reasonably sized job," manager Bruce Harvey said.
"The challenging part of the job was making allowances for the shape of the ceiling."
Knox Church finance committee convener Chris Bloore said the ceiling would be cleaned while the scaffolding was up.
"I don't think the ceiling has been cleaned since it was built."
Nor had it been dusted, with 6mm of dust piled above the beams, he said.
Pipes from the organ had been dismantled to make way for the scaffolding and would undergo maintenance before being refitted.
Work would begin next week on the restoration of the south-facing stained glass window, he said.
"Some of the faces in the window have faded, so we have been quite keen to have that remedied for some time."
"I took the minster around here the other day and she was just gobsmacked by how the church looks.
"It is a bit like people coming into your house to do renovations - it is quite hard to get used to."
Additional funding for the project had come from the synod and community funders.
During the three-month job, the congregation had moved to First Church and it "has been nice getting to know their congregation", Mr Bloore said.
