The man accused of killing Ballarat mum Samantha Murphy looks completely different after being held in protective custody behind bars.

Patrick Orren Stephenson, 23, fronted the Ballarat Magistrates’ Court on Thursday over the alleged murder of Ms Murphy.

Daily Mail Australia can reveal Stephenson, who appeared in court via video link, has bulked-up while in jail.

He has also shaved off the shaggy beard he sported after his arrest in March.

Stephenson appeared in person during his first court hearing soon after his arrest.

Dressed in bright orange tradesman gear, Stephenson was notably leaner at the time.

Since his arrest, Stephenson has been housed at the Melbourne Assessment Prison in the heart of Melbourne’s CBD.

It is understood the alleged killer has been held in protective custody, where he would be allocated a mere hour to exercise each day.

Dressed in a white T-shirt, it appeared that Stephenson has been using his spare time to lift weights.

Stephenson, who has no connection to the Murphy family, was charged with murdering the mother-of-three on March 7.

He is the son of former AFL player Orren Stephenson, who played 15 games for Geelong and Richmond between 2012 and 2014.

Patrick Orren Stephenson was himself a well-known footballer in the Ballarat region up until he was charged over the murder of Ms Murphy.

The court heard police had compiled a large brief of evidence against the alleged killer, which contained an ‘extensive amount’ of CCTV footage.

Stephenson’s lawyer, Moya O’Brien, told the court that both parties were seeking a three-month adjournment due to the sheer amount of evidence in the brief.

‘It has been described as unprecedented in size,’ she said.

Magistrate Mark Stratmann granted the request but expressed concern over the length of time considering Stephenson would remain behind bars.

‘Three months is quite a long time for your client and the community,’ he said.

The alleged killer did not show any emotion during his court appearance.

He sat quietly during the 15-minute hearing and only spoke once, when Mr Stratmann asked if he could see and hear the court.

‘Yes, your honour,’ he replied.

Stephenson will not return to court until November 16, when Mr Stratmann said he expected any issues in the case ‘to be ventilated’.

The court heard his defence team was working with prosecutors about narrowing down disclosure evidence to move the case along more quickly. 

Stephenson will again tune in via video link, sparing him from a potential stare-down with friends and family of Ms Murphy.

No one appeared to tune into the court link to support Stephenson.

Ms Murphy’s husband, Mick Murphy, was not spotted on the video link or in court on Thursday. 

Instead, he was seen at home tending to household duties. He declined to comment on the court case.

Ms Murphy vanished without a trace on the morning of February 4 after she left her home on Eureka Street in Ballarat East, Victoria.

The short hearing failed to produce any information on how police put their case against Stephenson.

Access to additional driving charges were denied to the media by the magistrate.

Ms O’Brien refused to comment on the case as she left the court.

While Stephenson’s arrest over the alleged murder provided some relief to the Ballarat community, it has failed to provide any answers to where Ms Murphy’s body was dumped.

Ms Murphy’s disappearance sparked a massive community effort over the following days to try and find her.

The 51-year-old set out for her morning run at 7 am through the nearby Woowookrung Regional Park—a 14km route she had done countless times before.

In early March, almost five weeks after Ms Murphy’s disappearance, police charged Stephenson with her alleged murder despite her body never being found.

On Sunday, Ms Murphy’s family, friends, and the wider Ballarat community marked six months since her disappearance.

Many were hoping this week’s hearing would begin to answer questions as to why Stephenson allegedly killed her.

The case is one of the highest priority criminal investigations for Victoria Police, with the missing persons squad working tirelessly to compile evidence for the expected trial.

A breakthrough in the case came after police searched a dam at a property south of Buninyong, approximately 14km from her home, on May 29.

Officers located a mud-splattered mobile phone in a wallet at the water’s edge, believed to have been found by a police tech detector dog.

In a statement issued shortly after the mobile phone was found, police said they had located some ‘items of interest’ during the search for the missing mum.

The phone, along with other items found in the search, underwent forensic testing with sources confirming the device belonged to Ms Murphy.

Many were hopeful the phone would lead to Ms Murphy’s body, however, police have remained tight-lipped on the evidence found on the device.

Police launched a series of ‘targeted searches’ in bushland and on properties across the area, with hopes of locating the missing mum’s body or finding crucial evidence to strengthen the case.

If a preliminary committal hearing goes ahead as expected, a Supreme Court of Victoria murder trial is unlikely to get underway until mid to late next year at best.

The process could be further delayed by fresh evidence being provided by homicide squad detectives, who continue to investigate the case in the hope of finding Ms Murphy’s body.

Police allege Stephenson ‘deliberately attacked’ Ms Murphy in Mount Clear, about 7km into her run.

It is understood Stephenson has reserved his right to silence.