Edgar's Mission in Kilmore has been under threat from fires since Sunday and staff activated their bushfire plan that afternoon.
Part of the plan involved evacuating some of the animals to safer areas, but Edgar's Mission founder Pam Ahern says finding somewhere to evacuate animals to can be difficult.
"You can try to evacuate, but where do you go to?" she said.
"Some people around the area evacuated to Kilmore racecourse, but then they had to evacuate [again].
"The whole of the state is really a potential fire risk so where to do you take them?"
The solution was for staff to take some of the animals home with them on Sunday night.
Almost 30 roosters, pigs, sheep, chickens and rabbits are now camping out in a suburban backyard in Ashwood in Melbourne.
But not all animals could be evacuated so Ms Ahern says she decided to stay on the farm.
"I couldn't leave the farm knowing that some of my animals were here to possibly perish through a fire or thereafter with lack of food, lack of water," she said.
The animals left on the farm, including sheep, cows and pigs, have been herded into a 'fire paddock' near the main house.
Ms Ahern says the animals did not seem too distressed.
"They all moved really calmly... everyone was really obliging," she said.
Other animals are also shacked up inside the house; one bedroom has essentially been transformed into a chicken hutch.
Two hours of sleep, one hour on watch
There are three people still on the farm working to keep it safe from the fires.
They have buckets and mops set out all over the farm and have been rotating overnight shifts to keep watch for any signs of fire.
"There was a spooky calm on the farm this morning when we got up. There's no wind, visibility immediate is OK, but all around us all we can see is smoke," Ms Ahern said.
She says the downtime has given her a chance to think about what is happening.
"I'm really nervous, I'm really quite scared at the moment because there's not a lot happening" she said.
"I think it's possibly harder for the people who've left because they're worried about me here, whereas in the last few days we've worry about the fires and putting out embers.
"We've been busy, we've been doing something all the time.
"We haven't slept in the last 24 hours."
The group has a large social media following and volunteers on the farm have been busy keeping their supporters updated on the situation.
"I'm just so incredibly touched that we mean so much to everyone," Ms Ahern said.
"Our priority has been protecting the farm... we've tried to keep people updated... but I'm a bit nervous to say 'we're fine' and then five minutes later the wind turns and we have a fire upon us."
The property so far has escaped any serious damage, although some people in the area have lost their homes.