A photograph of his pregnant partner printed on the front page of the Daily Telegraph has triggered a fierce debate about whether the image and accompanying article are an invasion of privacy or matter of public interest. But now his wife of 24 years, Natalie (pictured with her now estranged husband at top of page), has broken her silence to confirm the affair.
'I am deeply saddened by the news that my husband has been having an affair and is now having a child with a former staff member. I understand that this affair has been going on for many months and started when she was a paid employee,' she said.
'This situation is devastating on many fronts. For my girls who are affected by the family breakdown and for me as a wife of 24 years, who placed my own career on hold to support Barnaby through his political life.
'Our family life has had to be shared during Barnaby’s political career and it was with trust that we let campaign and office staff into our homes and into our lives. Naturally we also feel deceived and hurt by the actions of Barnaby and the staff member involved.
'The situation for myself and the girls will be made worse by the fact that this will all be played out in public so at this time, I would ask that the girls and I are given some privacy and time to come to terms with the consequences and take steps to plan our future.'
Rumours of the affair and baby surfaced during the New England by-election in October but had not been formally confirmed.
"It's something I view as none of my business," Labor frontbencher Tony Burke told reporters in Canberra on Wednesday.
"This ricochets and affects families. There's a principle here that I've always abided by to not engage in anything that hits the private lives of other members of parliament."
Greens MP Adam Bandt agreed, describing the prominent media coverage as a "very dark day" for gender equality.
"I don't really care who Barnaby Joyce or anyone else is sleeping with," he told Sky News.
"Unless it impacts on his job, or unless she chooses voluntarily to step into the public eye, it's not really anyone's business.
"If it's Barnaby Joyce's partner today, who else's will it be tomorrow?"
Cabinet minister Dan Tehan said the decision to put such information into the public domain should be up to the individuals involved.
However, gay rights campaigner Rodney Croome unloaded both barrels on the "hypocrite" deputy prime minister, who vehemently opposed same-sex marriage and demanded the issue be put to a national vote.
"You can't put the lives of tens of thousands of your fellow citizens under the microscope and then expect to avoid scrutiny yourself," Mr Croome said.
He argued the scandal exposed what "traditional marriage" meant for people like Mr Joyce.
"It is not a set of standards for heterosexual couples to live up to. It is a euphemism for prejudice against LGBTI people and our exclusion from the core institutions of society," Mr Croome said.
The staffer is Mr Joyce's former media adviser Vikki Campion, 33, according to News Corp.
The couple have reportedly moved in together, and their baby is due in April.
Mr Joyce, 50, has four daughters from his marriage to Natalie Joyce.
A version of this article was first published by Perth Now.