Over million years of evolution, gas dust and ice in protoplanetary disks can be chemically reprocessed. There is evidence that the gas-phase carbon and oxygen abundances are subsolar in disks belonging to nearby star forming regions. These findings have a major impact on the composition of the primary atmosphere of giant planets (but it may also be valid for super-Earths and sub-Neptunes) as they accrete their gaseous envelopes from the surrounding material in the disk. In this study, we performed a thermochemical modeling analysis with the aim of testing how reliable and robust are the estimates of elemental abundance ratios based on (sub)millimeter observations of molecular lines. We created a grid of disk models for the following different elemental abundance ratios: C/O, N/O, and S/O, and we computed the line flux of a set of carbon-nitrogen and sulphur-bearing species, namely CN, HCN, NO, C2H, c–C3H2, H2CO, HC3N, CH3CN, CS, SO, H2S, and H2CS, which have been detected with present (sub)millimeter facilities such as ALMA and NOEMA. We find that the line fluxes, once normalized to the flux of the 13CO J = 2−1 line, are sensitive to the elemental abundance ratios. On the other hand, the stellar and disk physical parameters have only a minor effect on the line flux ratios. Our results demonstrate that a simultaneous analysis of multiple molecular transitions is a valid approach to constrain the elemental abundance ratio in protoplanetary disks.