The Newcastle and Hunter Valley Speleological Society took both the Upper Hunter Shire Council and Stoneco Pty Ltd to the Land and Environment Court of NSW, challenging the council's approval for the quarry.

The conservationists said it would have a negative impact on endangered plants and animals including white box, yellow box, Blakely's red gum and the squirrel glider.

They estimated the quarry would remove 2.4 million tonnes of high-grade limestone from the hillside using drill and blast methods in more than 30 years.

The court decided last month it would allow development, subject to a long list of conditions.

Solicitor Natasha Hammond-Deakin from The Environmental Defenders Office, which represented the group in court, said it was a good outcome.

"The quarry will not be able to start blasting for at least a year as it is required to monitor for caves, voids, fissures and other geodiversity of significance," she said.

"[It also has to] sample for underground fauna species on the site and outside the site for at least one year before the first blast takes place."

Ms Hammond-Deakin said the quarry owner was required to conserve 60 hectares in the long term as an offset.

The Environmental Defenders Office also hoped the case would have flow-on effects.

"Use of ameliorative measures to reduce the likelihood of threatened species being significantly affected may increase as a result of this case and other cases," it stated.