Mission Local reports that graffiti scrawled on the window that was not shattered, read "Free Palestine."
Smitten's owner is Jewish, according to Mission Local.
MORE: San Francisco deals with increasing graffiti, tagging to private properties
San Francisco police found the windows smashed just before 3 a.m. when they went to check out an alarm at the Valencia Street shop.
Police say this is an active and ongoing investigation.