In the present study, we numerically investigate the effect of Prandtl number on the heat transfer mechanism in turbulent Rayleigh–Bénard convection inside a cubical box endowed with conical roughness elements. The Rayleigh number is kept fixed at Ra=108, while the Prandtl number (Pr) varies from 1 to 50. In contrast to the monotonic increasing trend of the Nusselt number (Nu∼Pr0.27) in the two-dimensional (2D) roughness explored previously [Sharma et al., “Influence of Prandtl number in turbulent Rayleigh-Bénard convection over rough surfaces,” Phys. Rev. Fluids 7, 104609 (2022)], it assumes an invariant behavior (∼Pr0.012) for three dimensional (3D), though it is approximately 50% higher than its smooth counterpart. Flow intensity, measured in terms of Reynolds number (Re), drops with increasing Pr showing consistently lower magnitude for the 3D configuration. The addition of roughness elements is observed to disrupt the preferred orientation of large-scale circulation (LSC). The effect is predominant for lower Pr, where the roughness interferes most with the natural bias of LSC toward the diagonal planes of the cubical box. The analysis of plume statistics reveals that both coverage and intensity of plumes are augmented for the roughened cell. Increased homogeneity in the flow at higher Pr is reflected by the emergence of a more pronounced and distinguishable peak in probability density functions of temperature and velocity. Temporal spectra and variance data substantiate augmented intensity of fluctuations in the rough cell, while behavioral differences in the flow at different Pr are elucidated by using cross correlation of vertical velocity and temperature fluctuations.