The BAPS Hindu Mandir, recently constructed in Abu Dhabi, UAE, is a complex unreinforced stone masonry structure built from thousands of sculpted sandstone and marble pieces employing ancient Indian techniques called Shilp Shastra. The entire structure is substantially large with a footprint size of 5,100 m2 and unique so that it is not covered by modern seismic design standards. Its performance was verified by conducting dynamic field tests presented herein. The most vulnerable substructure was identified based on both engineering judgement and modal analysis of the entire structure employing a detailed 3D finite element model, which was validated via the field experiments. A “local” model was developed for the identified vulnerable substructure which significantly reduced model complexity and allowed to overcome computational limitations. Based on the response of the local model, the relative importance of the sensor locations was determined via a Displacement Index method in addition to a reduction of the total variance of spectral accelerations using conditional probability theory. Through this approach, a methodology for selecting the optimal sensor placement with application on the complex unreinforced stone masonry Hindu Mandir is proposed.