Porphyrin-based metal-organic frameworks (MOFs), exemplified by the prototypical representatives MOF-525, PCN-221, and PCN-224 are among the most promising MOF systems for catalysis, optoelectronics, and solar energy conversion. However, subtle differences between synthetic protocols for these three MOFs give rise to vast discrepancies in purported product outcomes and description of framework topologies. Here, we reveal the type and disorder of the Zr-clusters based on a comprehensive synthetic and structural analysis spanning local and long-range length scales. Our analysis on PCN-221 reveals Zr6O4(OH)4 clusters in four distinct orientations within the unit cell, rather than Zr8O6 clusters as originally published, accompanied by random linker vacancies around 50%. We propose disordered PCN-224 (dPCN-224) as a unified model to understand PCN-221, MOF-525, and PCN-224 by varying the degree of orientational cluster disorder, linker conformation and vacancies, and cluster—linker binding. Our work thus introduces a new perspective on network topology and disorder in Zr-MOFs and pinpoints the structural variables that direct their functional properties.