York Regional Police say they were called Sunday night about the graffiti in front of the Jaffari Community Centre in Thornhill.
Among the messages spray-painted onto the sidewalk and entrance sign were "Arab go home" and vulgarities referencing the ongoing conflict in the Gaza Strip.
The incident happened about a week before the end of the Muslim holy month of Ramadan.
Police say the hate crime unit has taken over the case but there's no word yet on suspects.
The Islamic Shia Ithna Asheri Jamaat of Toronto, which runs the centre, says it is "disturbed" by the vandalism and that the incident comes a week after it hosted an interfaith event.
"While appalling, these actions do not represent the attitudes of Canada's multicultural society," the group said Monday in a statement.