In this paper, a vibration-based method to estimate prestress-forces in a prestressed concrete (PSC) girder by using vibration characteristics and system identification (SID) approaches is presented. Firstly, a prestress-force monitoring method is formulated to estimate the change in prestress forces by measuring the change in modal parameters of a PSC beam. Secondly, a multi-phase SID scheme is designed on the basis of eigenvalue sensitivity concept to identify a baseline model that represents the target structure. Thirdly, the proposed prestress-force monitoring method and the multi-phase SID scheme are evaluated from controlled experiments on a lab-scaled PSC girder. On the PSC girder, a few natural frequencies and mode shapes are experimentally measured for various prestress forces. System parameters of a baseline finite element (FE) model are identified by the proposed multi-phase SID scheme for various prestress forces. The corresponding modal parameters are estimated for the model-update procedure. As a result, prestress-losses are predicted by using the measured natural frequencies and the identified zero-prestress state model.