The disclosure is directed towards proxy services for the secure uploading of file-system tree structures. A method includes receiving, at a web security service, an indication that client device to upload content to a storage cloud provider. The proxy service performs a security scan of the content while the content is stored on the client device. A security and/or a privacy concern is identified in the content stored on the client device. A security and/or privacy mitigation action is performed in response to identifying the security and/or privacy concern.