Firefighters were called to Boleskine House, Foyers, on the south side of Loch Ness, around 3.30pm yesterday.
New owners took over the property last month with a pledge to restore the property, that was badly damaged by fire in 2015.
The Boleskine House foundation planned to open up part of the property to the public as well as create a wellness-style retreat where followers of Crowley's teachings could gather.
Police Scotland believe the fire was started deliberately and are appealing for witnesses.
Today, spokesman for the foundation said: "It is with great sadness that we report that the remainder of the building’s interior has now been destroyed, and along with it important historical clues to the features of this important piece of Scottish heritage.
"We would like to thank the fire fighters who put their lives at risk to save what is left of the building. We can also confirm that this is suspected arson and investigations by the police will be ongoing. Please support us to fund emergency works to protect the structure."
Crowley was said to have performed occultist rituals at the property when he lived there between 1899 and 1913.
The B-listed Georgian building was later owned by musician Jimmy Page, of Led Zeppelin.
Fires were reported at two buildings on the site, including the derelict main house and at an external outbuilding.
No one was injured in the fire.
Detective Inspector Eddie Ross said: "We are working with the Scottish Fire and Rescue Service to establish the full circumstances.
"Our enquiries are at an early stage, although our initial assessment is that this fire was started deliberately.
"We would encourage anybody may have seen any activity around Boleskine House or nearby to come forward as soon as they can.
"It should go without saying that deliberately setting fires is incredibly dangerous as you have limited control over how they may develop."
Boleskine house was built in the 1760s by Archibald Fraser, British consul in Tripoli and Algiers and member of Clan Fraser.
Crowley paid £2,000 for the secluded property, more than twice the market value of the day.
Boleskine became so important to Crowley that he taught his followers to focus their spiritual intent in its direction.
"For over a century, many people have considered Boleskine to be spiritually important, a magical place of sublime beauty," the foundation said.
The cost of restoring of the building has been estimated at £730,000 with the foundation saying the revival of Boleskine House will be a "loss-making endevour".
"Nevertheless, the buyers and volunteers or the project believe that Boleskine should be restored as a heritage landmark and opened to the public so that its history, spirit and legacy may be enjoyed for generations to come," the foundation said.
A crowdfunder has been launched to support the restoration of the property with a clearance weekend of the fire-damaged house organised for mid-August. Volunteers are expected to come from around the world for the event, it is understood. Money is now being sought for emergency repairs to make the property safe.
"Anyone with information about this fire can contact Police Scotland on 101, quoting incident 3619 of July 31, or call Crimestoppers anonymously on 0800 555 111."