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Gradual deterioration meant the Edwardian-styled glasshouse, built in 1908, needs a total refurbishment both inside and out.
All the plants will be removed before work begins.
Dunedin City Council operations manager parks and recreation Jendi Paterson said both the environmental condition and appearance of the glasshouse would be improved.
It was expected to cost about $368,000, she said.
The council had already asked for tenders. A combination of the warm, humid environment inside the building and exposure to the elements on the outside had caused the deterioration, Ms Paterson said.
Work would include glass replacement, repairs to window frames, doors, the metal structure, painting, floor levelling and drainage.
Regular maintenance was completed annually but the last time this level of work was required was in 1990, Ms Paterson said.
Botanic Garden team leader and curator Alan Matchett said the refurbishment provided an opportunity to explore different ways of displaying the plants.
The glasshouse would be closed during the refurbishment and there was no expected completion date, Mr Matchett said.
"Once the contractors can get in and have a look they will have a better idea, but we don’t expect it to take too long," he said.
For the past two months, winter garden glasshouse curator Stephen Bishop and his team have been taking cuttings from plants inside the glasshouse and growing them at the botanic garden’s propagation facility.
If possible, larger plants such as palms would also be moved to the facility, Mr Bishop said.
"It’s going to be really interesting and it’s good to have changes to keep people interested in what is happening. We’re going to be changing up some of the displays as well."
Growth inside the glasshouse was quick so it would not take long for it to fill out again, he said.
Before any work started, the garden’s rare Amorphophallus titanum, better known as a corpse flower, would be allowed to bloom.
"We’ve got it on display down here now and it’s just piling on the growth each day — about 5 or 6 centimetres each day — but we still don’t know when it will bloom yet," Mr Bishop said.