Nova Scotia Supreme Court Justice Patrick Murray ruled Thursday on an injunction request by the agency.
The decision came after five days of testimony earlier this month over the way the Cape Breton Human Society has been run.
Volunteers and staff with the provincial SPCA told the court that they had serious concerns over cases of animal neglect and a failure to provide veterinary care at the shelter.
The local board said it was largely unaware of those concerns and that many of the allegations were based on hearsay.
"I've been here for eight years," said Barbara Larick, one of the volunteers at the shelter.
"I wouldn't be here if we were doing everything that they were saying."
Kristin Williams, director of the provincial SPCA, said lawyers are discussing how the handover will take place.
"We have staff on standby to come up, including our provincial veterinarian," she told CBC News.
"Our immediate concern will be to turn our attention to the shelter, make sure all the animals are OK, implement new protocols and procedures and start to improve the operations of that facility."
Williams said she is prepared to stay in Sydney over the weekend to help things go smoothly.
Sydney shelter workers, volunteers upset
Within an hour of the judge's decision, Williams was at the shelter to meet with the staff members — many of whom were upset and crying.
"This is obviously going to be a difficult situation for them. I'm sure they're going to be quite stressed by this level of transition and I'm very sensitive to that," she said.
Williams said with the exception of Patsy Rose — the shelter's manager — the workers can keep their jobs as long as they agree to live up to the provincial SPCA's standards.
"If that's not possible then we'll have to review that but we're very clear about our standards and that's partly why we're here, because we want to implement a higher standard and they're going to need to be able to demonstrate that they can achieve that," she said.
"Patsy Rose will not be continuing after today."
Mark Mombourquette, the chair of the Cape Breton Humane Society, said the board is disappointed by the court decision but respects it.
"We're all here first and foremost for the animals, it's one of those things that we will get through," he said.
"Everybody is very, very emotional so we just want any questions that the staff had or any questions that Kristin had, we were there to answer them to best of our ability."
In November, the provincial body voted to dissolve the Cape Breton branch and fired Rose. When it tried to take over the shelter, the workers refused to leave.
The local branch, now called the Cape Breton Humane Society, is fighting to retain ownership of the shelter. The two sides will return to court later to argue over permanent control.