The main aim of this paper is to realize for the first time the effect of nanofluid preparation method on the performance of photovoltaic/thermal (PV/T) system in a comparative experimental study. Silver nanofluid via one-step and two-step method at different concentrations of 1%, 3%, and 5% were prepared. The stability of nanofluid at all concentrations was measured via zeta-sizer before and after experiments and the results showed the stability of nanofluid in one-step prepared is significantly higher than two-step. It was elucidated that the energy and exergy of the PV/T for one-step nanofluid substantially improved compare to the two-step preparation method. Moreover, it was found that by increasing nanofluid from 1 to 3% and 3 to 5% in one-step method all efficiencies were linearly increased but for two-step prepared nanofluid the maximum rate of enhancement was obtained from 1 to 3%. It was observed that when system operated with two-step prepared nanofluid, performance of the system for 3% at turbulent-flow regime is higher than 5% at laminar-flow regime which directly related to the stability of nanofluid. Based on our results it can be concluded that nanofluid preparation method and its stability also play crucial roles on the performance of PVTs.