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In the synthesis of complex oxides, solid-state metathesis provides low-temperature reactions where product selectivity can be achieved through simple changes in precursor composition. The influence of precursor structure, however, is less understood in solid-state synthesis. Here we present the ternary metathesis reaction (LiMnO2 + YOCl → YMnO3 + LiCl) to target two yttrium manganese oxide products, hexagonal and orthorhombic YMnO3, when starting from three different LiMnO2 precursors. Using temperature-dependent synchrotron X-ray and neutron diffraction, we identify the relevant intermediates and temperature regimes of reactions along the pathway to YMnO3. Manganese-containing intermediates undergo a charge disproportionation into a reduced Mn(II,III) tetragonal spinel and oxidized Mn(III,IV) cubic spinel, which lead to hexagonal and orthorhombic YMnO3, respectively. Density functional theory calculations confirm that the presence of Mn(IV) caused by a small concentration of cation vacancies (∼2.2%) in YMnO3 stabilizes the orthorhombic polymorph over the hexagonal. Reactions over the course of 2 weeks yield o-YMnO3 as the majority product at temperatures below 600 °C, which supports an equilibration of cation defects over time. Controlling the composition and structure of these defect-accommodating intermediates provides new strategies for selective synthesis of complex oxides at low temperatures.