Systems and methods for overlay-based file tagging using virtual file systems. An example method may include: receiving, from a file system client, a request to perform a file operation with respect to a file; identifying a part of the file name representing a mount point of a virtual file system associated with the file; identifying a memory pointer associated with the mount point; identifying, using the memory pointer, an instance of a class implementing the virtual file system; retrieving the metadata associated with a file using a memory data structure associated with the instance of the class, the memory data structure comprising a plurality of records, each record associating a file identifier with a metadata item; and performing the file operation using the metadata associated with the file.