Methods, systems, and media for protecting computer systems from user-created objects are provided. In some embodiments, the method comprises: detecting, at a second user device, that an object has been accessed on the second user device; determining whether an exception has occurred by scanning the object on the second user device; in response to determining that the exception has occurred, transmitting, from the second user device to a server, a request for a security policy to be applied by the second user device in connection with the object, wherein the request includes an identifier of the object; receiving, from the server, the security policy; determining, based on the security policy, that the object was created by a first user device associated with an organization the second user device is also associated with; determining whether to allow the object to be accessed by the second user device based on the security policy; and in response to determining that the object is allowed to be accessed, allowing the object to be accessed on the second user device.