A method and system for handling a plurality of applications in a Near Field Communication (NFC) device is provided. The method is performed at a NFC Controller (NFCC). The method includes storing a source host identity (ID), a destination host ID and a link ID associated with each application from one or more applications. The method also includes managing the one or more applications simultaneously based on the source host ID, the destination host ID and the link ID stored in the NFCC. Problem : how to manage multiple NFC applications on an NFC device simultaneously. Solution : a plurality of applications associated with a Device Host and corresponding Secure Elements are managed by a NFC Controller (NFCC) by creating - logical links . A logical link is used to identify a communication path between the NFCC and the applications residing in the DH, SE or with a remote NFC device. The NFCC manages the applications simultaneously based on the source host ID, the destination host ID and the link ID stored