Dr Yehu Azaz, 50, says he was "unduly influenced" by Rena Denton into signing away his entire estate to her Self Realization Meditation Healing Centre.
He claims he gave up his medical career to join her band of followers and the gifts were loans which he expected to be repaid when he left.
The bulk of his case was dismissed by the High Court on Tuesday but he was allowed to continue with a small claim for the return of £35,000 of personal belongings.
During a hearing earlier this month it was claimed that Dr Azaz and his then wife donated everything they owned to the registered charity shortly after joining in the early 1990s.
But more than a decade later in 2003, Dr Azaz, who changed his name to Simon during his time as a "disciple", left the group and suffered a nervous breakdown, the court was told.
He tried suing for the return of the money he donated as well as breach of contract and "personal injury", including lost earnings as a doctor while he worked at the centre for little or no pay.
He claimed the assets he handed over were loans which he believed would be repaid if he left.
During the trial his lawyer, Evan Ashfield, said there was an "extremely strong" case he would not have given away everything had it not been for Mrs Denton's "presumed undue influence" as his guru.
But Mrs Denton, known as Mata Yogananda Mahasaya Dharma, and the centre she runs in the village of Queen Camel, near Yeovil, Somerset, denied any wrongdoing throughout the hearing.
His Honour Judge Seymour QC dismissed the overwhelming majority of Dr Azaz's claim on the basis that these claims had been brought many years too late.
A statement from Miss Denton's solicitors Carter-Ruck said: "His Honour Judge Seymour QC has also made it clear that, quite apart from the limitation problems, many of the claims brought by Dr. Azaz were either factually or legally unsustainable (and in some instances both)."
Dr Azaz was ordered to pay the Centre's legal expenses.
Mrs Denton's solicitor, Edward Yell, from Carter-Ruck, said: "These proceedings have been a source of great concern and a significant burden to all involved with the Centre for many months.
"The Self Realization Meditation Healing Centre is delighted to put this unfortunate episode behind them and very much looks forward to getting back to its work promoting the art and science of meditation and healing and helping all who are in need."
Dr Azaz is now working as a trainee GP in Thame, Oxfordshire.
