JasperImageThe foundation said the community centre and main sanctuary were destroyed. No-one was injured.
Joseph Clark, 49, of Elgin, appeared at Inverness Sheriff Court charged with wilful fireraising. He made no plea and was remanded in custody.
About a dozen people were safely evacuated as firefighters tackled the blaze at about 02:00.
The Findhorn Foundation was formally registered as a Scottish charity in 1972, 10 years after it began life with just a single caravan.
The foundation – described as an international spiritual education centre – has welcomed thousands of people from all around the world over the last 59 years.