Phase control in the self-assembly of metal-organic frameworks (MOFs) is often a case of trial and error; judicious control over a number of synthetic variables is required to select the desired topology and control features such as interpenetration and defectivity. Herein, we present a comprehensive investigation of self-assembly in the Fe-biphenyl-4,4′-dicarboxylate system, demonstrating that coordination modulation can reliably tune between the kinetic product, non-interpenetrated MIL-88D(Fe), and the thermodynamic product, twofold interpenetrated MIL-126(Fe). Density functional theory simulations reveal that correlated disorder of the terminal anions on the metal clusters results in hydrogen-bonding between adjacent nets in the interpenetrated phase and is the thermodynamic driving force for its formation. Coordination modulation slows self-assembly and therefore selects the thermodynamic product MIL-126(Fe), while offering fine control over defectivity, inducing mesoporosity, but electron microscopy shows MIL-88D(Fe) persists in many samples despite not being evident by diffraction. Interpenetration control is also demonstrated using the 2,2′bipyridine-5,5′-dicarboxylate linker; it is energetically prohibitive for it to adopt the twisted conformation required to form the interpenetrated phase, although multiple alternative phases are identified due to additional coordination of Fe cations to its N-donors. Finally, we introduce oxidation modulation-the use of metal precursors in different oxidation states to that found in the final MOF-to kinetically control self-assembly. Combining coordination and oxidation modulation allows the synthesis of pristine MIL-126(Fe) with BET surface areas close to the predicted maximum for the first time, suggesting that combining the two may be a powerful methodology for the controlled self-assembly of high-valent MOFs. linkers used in this study. b) Packing structure of the twofold interpenetrated MIL-126(Fe), with the distinct nets coloured red and blue. Redrawn from CCDC deposition MIBMER. 14 c) Packing structures, viewed down the c axis, of open and closed MIL-88D(Fe), generated from simulated structures (not to scale), C: grey; O: red; Fe: orange spheres; H atoms removed for clarity.