A computing system may include a EMM server having a metadata anonymization policy associated therewith, and a client computing device configured to generate metadata and combine the metadata with respective user content data, with the client computing device having a metadata permission policy associated therewith. The client computing device may be further configured to enroll with the server, determine user content data having metadata combined therewith in violation of the metadata anonymization policy, and when the metadata permission policy permits separation of the metadata from the user content data, strip the metadata from the user content data so that the metadata is inaccessible when the user content data is accessed.