Elders general manager David Goodfellow has quit the company just weeks after being controversially overlooked for the position as chief executive.
The move comes after Mark Allison made the highly unusual decision to step down as chairman to become chief executive.
In explaining the selection process which was criticised by the Australian Shareholders' Association, Mr Allison took a veiled swipe at the quality of other candidates.
He said the board was not convinced the other candidates, including Mr Goodfellow, had the ability to "make Elders better off".
Mr Goodfellow, who ran more than 200 branches and other operations, was silent on his sudden departure.
He was recruited to Elders from Macquarie Bank's Paraway Pastoral by former managing director Malcolm Jackman in 2011 and anointed as CEO-in-waiting.
The Elders board snubbed a short list of four candidates following what it described as an intensive six-month search, before it appointed Mr Allison.
An Elders spokeswoman said Mr Goodfellow had made a significant contribution in the move back to a pure play agribusiness.
Last week, Elders reported a $10.2 million loss for the six months to March 31.
It marked a big improvement on the $303 million loss, including $280 million in writedowns, from the same period last year.
In an update to staff, Mr Allison said the turnaround to an underlying profit of $6.7 million had attracted a lot of attention from analysts and investors. He said the decision to engage in another round of asset sell-offs had not been taken lightly.
Elders is selling its 50 per cent stake in Australian Wool Handlers and its New Zealand network. Other assets on the market are Charlton Feedlot in Victoria and the New Zealand wool trading business
Mr Allison said Elders would remain a valued customer of AWH and have unchanged access to its services. He said Charlton had been operating under capital constraints, which held it back.