The "regionally significant" stone oven, 3.9m long and 3m wide, was the best-preserved example of a 19th-century industrial oven remaining on a Clutha basin goldfields site, New Zealand Historic Places Trust archaeologist Matthew Schmidt said.
It was buried under what looked like a heap of dirt at the back of the 1872 building.
"It was a really good surprise, a real bonus find. We had no idea that much of the oven was left, " Dr Schmidt said.
The oven was built by James Lawrence, who also built commercial ovens at other 19th-century goldfields in the area, but none of the other ovens were known to have survived.
Dr Schmidt said the bakery "fed the Bendigo goldfields".
"This was the commercial hub of Bendigo and the bakery was on the main street."
The town was abandoned in the late 1930s and the remaining buildings at that time were progressively stripped of their stone, iron and timber.
The oven would have been wood-fired and had 60cm-thick walls, insulated with earth.
Four agencies are working together on stabilising and preserving the ruins, 20km from Cromwell.
The bakehouse is all that remains of the once-flourishing Bendigo township.
The building is on a Department of Conservation reserve, and Doc, the Otago Goldfields Heritage Trust, Otago Polytechnic stonemasonry students and the New Zealand Historic Places Trust are all involved in the project.
Dr Schmidt and Doc archaeologist Shar Briden spent three days on site and the oven was the most exciting find, Dr Schmidt said.
The structure has only been partially unearthed but the oven's side walls are visible.
Soil covers the top of the oven and will be left in place.
"These days, we don't go in and excavate a site just for the sake of excavating. It can be too destructive and expose the structure to the weather and to fossickers. It's nice to leave it a bit of a mystery."
