According to CEO John Warlters, the couple made the decision to depart to pursue other opportunities after assisting with the transition of roles in recent months.

Mr Warlters, formerly Australian Community Media's agricultural head, was appointed to the CEO's role at the end of February.

According to a statement at the time, Charles and Tracy Alder remained integral parts of Rural Aid.

On Wednesday afternoon, Rural Aid chairman Alex Hutton said the Alders will always be recognised for their contribution to the foundation of the charity, which is now assisting farmers and rural communities across Australia.

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"The team acknowledges and thanks co-founders Charles and Tracy Alder for their dedication to Australia's farmers and their communities," he said.

They founded Rural Aid in 2015 along with Sandra Walker, founding board director, who continues to be an integral part of the donor and Farm Army team.

Rural Aid has grown to become one of Australia's largest rural charities, built on the success of the Buy a Bale campaign.

Mr Warlters said the resignation had taken place last Friday and the team had been advised that afternoon.

He said the focus now was to deliver back to rural communities.

"We acknowledge the past and focus on the future," he said.

Mr Alder declined to comment, except to say that he and Tracy were very happy.

Rural Aid had been the subject of an inquiry by the Australian Charities and Not-for-profits Commission since November 2018, along with Aussie Helpers, following complaints around how it distributes its resources.

After a six-month inquiry, Aussie Helpers was cleared of inappropriate financial conduct, and Mr Warlters has confirmed that Rural Aid had met all obligations required of it by ACNC at the start of April this year.

He said these related to internal processes from a governance perspective.

"We had to make sure everything they were looking for was delivered," he said.

A spokesman for the ACNC said there were secrecy provisions in the legislation that established the ACNC that prevented them from being able to disclose information about individual charities.

"When the ACNC undertakes an investigation we work with charities to resolve identified issues.

"Certain outcomes of investigations, as well as certain details, can be published on the ACNC website.

"There are instances where the ACNC requires certain actions and improvements from a charity to finalise an investigation.

"When the ACNC is satisfied that a charity has met the required conditions, it will finalise an investigation."