Mixed convection of an electrically conductive fluid in a square duct with imposed transverse magnetic field is studied using Large Eddy Simulation (LES) paradigms. The duct walls are electrically conductive, with the wall conductivity parameter c_w ranging from 0 to 0.5. The Reynolds number is Re=5602 and the Prandtl number is Pr=0.0238. The focus of the study is on flows at Hartmann numbers Ha⩽125, Richardson numbers Ri⩽10 and two different thermal boundary conditions are considered: four wall uniform heat fluxes and one-sided heating (fixed wall temperature). The results show that the transition from laminar to turbulent flow depends not only on the ratio Ri/Ha, but also on c_w and on the local thermal boundary conditions. In the turbulent regime with one-sided heating, the turbulent heat fluxes play an important role in the total heat transfer, in contrast with the typical behaviours of liquid metals. Moreover, the turbulent and thermal structures are highly dependent on the thermal boundary conditions, which completely alter the flow structure. It is also found that at c_w≥0.01 the turbulent heat fluxes decrease.