The effect of doping in Si3N4 membranes on the secondary electron yield is investigated using Monte Carlo simulations of the electron-matter interactions. The effect of the concentration and the distribution of the doping in silicon rich silicon nitride membranes is studied by using the energy loss function as obtained from ab initio density functional theory calculations in the electron scattering models of the Monte Carlo simulations. An increasing doping concentration leads to a decreasing maximum secondary electron yield. The distribution of the doped silicon atoms can be optimised in order to minimize the decrease in yield.