Giant magnetocaloric (GMC) materials constitute a requirement for near-room-temperature magnetic re-frigeration. (Fe,Mn)2(P,Si) is a GMC compound with strong magnetoelastic coupling. The main hindrance towards application of this material is a comparably large temperature hysteresis, which can be reduced by metal site substitution with a nonmagnetic element. However, the (Fe,Mn)2(P,Si) compound has two equally populated metal sites, the tetrahedrally coordinated 3 f and the pyramidally coordinated 3g sites. The magnetic and magnetocaloric properties of such compounds are highly sensitive to the site-specific occupancy of the magnetic atoms. Here we have attempted to study separately the effect of 3 f and 3g site substitution with equal amounts of vanadium. Using formation energy calculations, the site preference of vanadium and its influence on the magnetic phase formation are described. A large difference in the isothermal entropy change (as high as 44%) with substitution in the 3 f and 3g sites is observed. The role of the lattice parameter change with temperature and the strength of the magnetoelastic coupling on the magnetic properties are highlighted.