Richard Curtis, 53, a military intelligence specialist, whose wife, Fiananda, 48, is also a former RAF officer, joined the Self Realization Meditation Healing Centre after he left the services.
The couple gave the farmhouse to the centre which is run by Rena Denton, whose post spiritual name is Mata Yogananda Mahasaya Dharma.
Cardiff Civil Courts of Justice heard Mr Curtis left the centre after discovering that his wife was having an affair with another man.
He sued the centre for the return of the house in the Welsh countryside, claiming that he had been "brainwashed" into parting with it.
The court ruled Mr Curtis had been "unduly influenced" into giving his home away, and was therefore entitled to his share.
Mr Curtis will now enter a mediation process with the healing centre, where his estranged wife is still a member.
It is expected the property known as Edwinsford, near Llandeilo, Carmarthenshire, will be sold with most of the proceeds shared between Mr Curtis and his wife.
The court heard the couple had been members of the centre for 11 years when they decided to give their home to the centre.
The centre, based in Queen Camel, near Yeovil, Somerset, has used the house as a "sister centre".
Nestling in a quiet wooded valley by the river Cothi, the centre advertises the property as "a wonderful base for walking, enjoying the peaceful communion with nature, and an idyllic retreat."
The main house was once in part, a large medieval Welsh longhouse.
The court heard Miss Denton gave the couple a book in which she wrote: "There's so much more to give. As you give you receive. Produce, land or money can be given to help or feed others."
Mrs Curtis, a mother-of-one, wanted to concentrate on working for the centre full time at the house.
Judge Milwyn Jarman, QC, said: "Mrs Curtis considered setting up special healing clinics and workshops at Edwinsford.
"Rena Denton had given her blessing to it becoming a sister centre and everyone was very joyous and emotional about the news.
"In April 2004 the declaration of trust was drawn up and signed by Mr and Mrs Curtis. They had not taken legal advice."
The court heard the agreement meant the group had financial rights to the house and began using it for meditation groups and workshops.
But in 2008 the couple decided to divorce after Mrs Curtis had an affair with another man, who was not a member of the organisation.
Mr Curtis later left the organisation and began proceedings to win back his house.
Judge Jarman said: "Mr and Mrs Curtis were giving away all they had; in my opinion the agreement was manifested to be disadvantageous.
"When he signed the declaration of trust in 2004, the group was in the position of spiritual adviser to Mr Curtis.
"Mr Curtis claims there was an undue influence on the behalf of the centre and I accept this but on the evidence I have heard there's no clear indication of brainwashing."
Mr Curtis, a specialist in Arabic languages, declined to comment after the hearing. The centre could not be contacted for comment.
Eighteen months ago, a doctor who claimed he was brainwashed into handing over £750,000 to the centre lost a claim for £2m damages.
Dr Yehu Azaz, 50, said he was "unduly influenced" by Miss Denton into signing away his entire estate to the centre.
He said 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.
But the bulk of his case was dismissed by the High Court on the basis that his claims had been brought many years too late.
The centre was established in 1988 by Miss Denton in response "to the needs of the age we live in".
