This, the second in a series of articles present a new framework for considering the computation of uncertainty in electron excited X-ray microanalysis measurements, will discuss matrix correction. The framework presented in the first article will be applied to the matrix correction model called “Pouchou and Pichoir's Simplified Model” or simply “XPP.” This uncertainty calculation will consider the influence of beam energy, take-off angle, mass absorption coefficient, surface roughness, and other parameters. Since uncertainty calculations and measurement optimization are so intimately related, it also provides a starting point for optimizing accuracy through choice of measurement design.