The use of second-order Jahn-Teller active Mo-VI centers and chiral organic amines is discussed as an approach to crystallographic noncentrosymmetry. Several series of reactions, conducted under mild hydrothermal conditions, were designed to probe important reaction variables. Correlations between reagent and solvent concentrations and the molybdate structure were investigated using composition space analysis, which allows for the isolation of specific reaction variables. The effects of amine structure variation were probed using multiple series of related amines, which consisted of either linear diamines or ethylenediamine derivatives. The addition of fluoride results in the loss of amine-based structural variations. Chiral organic amines were used to demonstrate the viability of using such components to control the three-dimensional symmetry in new materials. The synthesis, structure, and characterization of eight new organically templated polyoxomolybdates and polyoxofluoromolybdates are reported.