A method and system for providing secure peer-to-peer file transfers whereby request/negotiation message mechanisms used to negotiate file transfers between peers is used to identify/intercept, and block, direct file transfers. The request/negotiation messages are then replaced with messages sent to both peers that include upload and download URL links through which the file can be uploaded, scanned analyzed, and then transferred, via a secure file transfer server. Using the method and system for providing secure peer-to-peer file transfers disclosed herein, peer-to-peer file transfer transactions are provided protection from malware, and provided additional data security, so that peer-to-peer users can utilize this important capability without taking unacceptable risks.