The effects of atomic short-range order on the properties of Pb(Zr(1-x)Ti(x))O3 alloy in its morphotropic phase boundary (MPB) are predicted by combining first-principles-based methods and annealing techniques. Clustering is found to lead to a compositional expansion of this boundary, while the association of unlike atoms yields a contraction of this region. Atomic short-range order can thus drastically affect properties of perovskite alloys in their MPB, by inducing phase transitions. Microscopic mechanisms responsible for these effects are revealed and discussed.