The words “Saracen go home” and “Deus Vult”, a Latin term meaning "God wills it" , were found spray painted on the walls of the mosque in the North Lanarkshire town of Cumbernauld on Saturday morning.
The terms allude to the Crusades, when they were used by Christian soldiers and writers, but have become popular with far-right groups in recent years and appeared in racist graffiti in the US.
Police Scotland are treating the incident as a hate crime, and believe it took place between 9pm on Friday and 7.30am on Saturday.
Azhar Din, a trustee of the Islamic Education Trust Cumbernauld, which runs the mosque, said several CCTV cameras cover the building and the footage is currently being examined.
He said: “The graffiti has been sprayed on two of the walls and was noticed this morning. It was discovered when the first people arrived for morning prayers at about half past seven this morning.
"It has been reported to the police. It is very unusual to have this kind of thing in Cumbernauld and people are very worried by it."
Mr Din added that it was an “isolated incident” and that generally the community was “very supportive”.
"We have had a few isolated incidents - we've had windows broken and stones thrown - but nothing major,” he said.
"We have isolated incidents which happen when something kicks off in the news but we have more or less been quite fortunate and people have generally been supportive.”
A Police Scotland spokesperson said: “We can confirm that an investigation is under way following an act of vandalism at the Islamic Education Trust (mosque) in Cumbernauld and inquiries are continuing.
"This matter is being treated as a hate crime. Hate crime remains a priority for Police Scotland and we are working closely with our criminal justice partners to do everything in our power to protect all communities and eradicate all forms of hatred.”Reuse content