Using detailed synchrotron diffraction, magnetization, thermodynamic and transport measurements, we investigate the relationship between the mixed valence of Ir, lattice strain and the resultant structural and magnetic ground states in the geometrically frustrated triple perovskite iridate Ba₃NaIr₂O₉. We observe a complex interplay between lattice strain and structural phase co-existence, which is typically not observed in this family of compounds. The low temperature magnetic ground state is characterized by the absence of long-range magnetic order, and points towards the condensation of a cluster glass state from an extended regime of short range magnetic correlations.