Police and fire crews were called to the Guru Nanak Gurdwara in Sheriff Brae at around 5am on Tuesday. No-one was injured.
A 49-year-old man was arrested on Wednesday and Police Scotland said he has now been charged over the incident.
He has also been charged in connection with a second fire at The City of Edinburgh Methodist Church in Junction Place which also happened in the early hours of the same day.
The man is due to appear at Edinburgh Sheriff Court on Thursday.
The gurdwara, situated in a former church, is the only Sikh centre in the Scottish capital, serving a community of more than 500 people.
A Police Scotland spokesman said: “A man has now been charged following the suspicious fire at the Sikh Temple in Sheriff Brae, Edinburgh.
“The 49-year-old is due to appear at Edinburgh Sheriff Court on Thursday 30th August, where he will also appear in relation to a second fire at the Methodist Church in Junction Place which also happened in the early hours of Tuesday 28th August.”
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