Constructed in 1873 to house healthy married couples until they were cleared to enter Dunedin, the block has been under restoration by the St Martin Island Community for many years.
Trust chief executive Keith Ellwood said it was a significant investment for the trust, "one which acknowledges an important part of early Dunedin settlement".
The restored windows and joinery were due to be transported by helicopter back to the island this morning, allowing work to begin on making the building watertight.
"It's ... exciting," former Quarantine Island caretaker Kathy Morrison said.
In recent times, the building had been given a new roof and its ventilation shafts had been restored.
Work had also begun on restoring the walls of the wooden building.
The building was "wrapped up" after the weatherboards were taken off for preservation or replacing until the community could afford to get the windows and doors done.
Once it had confirmation of the trust's funds, it had the windows restored and reglazed in Dunedin.
The building would then be reclad and the windows installed, making it weathertight for the first time in many years, she said.
It was hoped the process would only take about two months.
The community also received $188,000 from a Lottery fund for the restoration.
Once the building was weatherproof, the floor would be mended so the building was usable.
There had already been requests from people keen to use it, she said.
The community then planned to have a rest and discuss the possibilities for the interior of the building, Ms Morrison said.
