We provide the first combined experimental and theoretical evaluation of how differences in ligand structure and framework topology affect the relative stabilities of isocompositional (i.e., true polymorph) metal organic frameworks (MOFs). We used solution calorimetry and periodic DFT calculations to analyze the thermodynamics of two families of topologically distinct polymorphs of zinc zeolitic imidazolate frameworks (ZIFs) based on 2-methyl- and 2-ethylimidazolate linkers, demonstrating a correlation between measured thermodynamic stability and density, and a pronounced effect of the ligand substituent on their stability. The results show that mechanochemical syntheses and transformations of ZIFs are consistent with Ostwald's rule of stages and proceed toward thermodynamically increasingly stable, more dense phases.