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The competing crystal field splitting, spin-orbit coupling, on-site Coulomb interaction, and Hund’s coupling lead to many novel electronic and magnetic states in the 5d transition metal based oxides, otherwise expected to be relatively simple metals (Annu. Rev. Condens. Matter Phys. 7, 195 (2016)). We present a hitherto unreported Ba₃CoIr₂O₉, stabilizing in the hexagonal P6₃/mmc symmetry at 300K, it exhibits a magneto-structural transition to a monoclinic C2/c phase at 107 K – the highest known amongst all the triple perovskite iridates. Below 70 K, a part of the system transforms to a monoclinic phase with even lower symmetry (P2/c), and both these phases coexist down to the lowest measured temperatures. We observe a negative thermal expansion in this phase co-existence regime, driven by magnetic exchange striction, and is of relevance to a number of systems with pronounced spin-orbit interactions. Both theory and experiments indicate that the Ir5+ carries a finite magnetic moment, suggesting that the putative J = 0 state is avoided. Heat capacity, electrical resistance noise and dielectric susceptibility all point towards the stabilization of a highly correlated ground state in this system.