"It is all now in the hands of the court. It's a very sad end to a highly successful partnership," said Emma.
Maher, 30, from Essex, has many fans in showjumping and has spent much of the year as the world's number one rider.
A spokesman for his lawyers declined to comment on the case at this stage.
Ben Maher factfile
30 January 1983
Tripple X, Cella, Aristo Z, Cloud 9, Robin Hood, Rolette
Beijing 2008, London 2012
Two claims from the couple - who run Quainton Stud in Aylesbury, Buckinghamshire - have been lodged at the Chancery Division of the High Court and outline the allegations against Maher.
They say he acted as agents for them in the buying and selling of horses, but secretly made money on some deals by giving them incorrect details of the prices paid.
He is alleged to have told the Phillips one of their horses, Tackeray, had been sold to a buyer in the United States for $500,000 rather than what they say is the actual sum of $850,000.
"Mr Maher thereby made a secret profit of $350,000 of which Mr Maher is accountable and to which Quainton Stud is entitled," says the court document.
It describes an invoice of $50,000 for third party commission on the deal as "a sham".
The showjumper is accused of making a secret profit or benefit on five other horses: Quainton Quirifino (10,000 euros), Awanti (50,000 euros), Vigolo (152,000 euros), Robin Hood (£80,000) and Wonderboy (£222,496).
In current conversion rates, the total amounts to nearly £700,000, although the financial impact of the case could be double that if any costs and damages were to be awarded.
Showjumper Ben Maher wins thrilling jump-off at inaugural Grand Prix of London
The Phillips say they have worked with the rider since 2005 when he was aged 22 and treated him "as one of the family".
Maher is said to have sold a half share in his Olympic horse Tripple X to them, and they enjoyed his success as part of the British victory in 2012.
But the relationship broke down earlier this year, and as part of their second civil action, the couple want to see Tripple X sold.
"We did all we could to provide the conditions that led to Ben's fantastic success at the Olympics last year and now feel broken-hearted," said Emma.
It is understood the practice of a jockey riding, training and acting as bloodstock agent is not unusual, and the case could have wider ramifications in equestrian sport.
"We love the sport. We adore our horses - but, in truth, we've become totally disillusioned," added Emma.
Maher has enjoyed a rise through showjumping's rankings and his successful 2013 has included being part of the British team that won the Dublin round of the Nations Cup. He was also victorious in the King George V Gold Cup at Hickstead.
He won team gold at London 2012 alongside Brash and Nick Skelton, then 54, and Peter Charles, 52.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.