Phase control in the self-assembly of metal-organic frameworks (MOFs) – materials wherein organic ligands connect metal ions or clusters into network solids with potential porosity – is often a case of trial and error. Judicious control over a number of synthetic variables is required to select for the desired topology and control features such as interpenetration and defectivity, which have significant impact on physical properties and application. Herein, we present a comprehensive investigation of self-assembly in the Fe-biphenyl-4,4'-dicarboxylate system, demonstrating that coordination modulation, the addition of competing ligands into solvothermal syntheses, can reliably tune between the kinetic product, non-interpenetrated MIL-88D(Fe), and the thermodynamic product, two-fold interpenetrated MIL-126(Fe). DFT simulations reveal that correlated disorder of the terminal anions on the metal clusters in the interpentrated phase results in H-bonding between adjacent nets 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 the MIL-88D(Fe) phase persists in many samples despite not being evident in diffraction experiments, suggesting its presence accounts for the lower than predicted surface areas reported for samples to date. Interpenetration control is also demonstrated by utilizing the 2,2'-bipyridine-5,5'-dicarboxylate linker; DFT simulations show that it is energetically prohibitive for it to adopt the twisted conformation required to form the interpenetrated phase, and are confirmed by experimental data, although multiple alternative phases are identified due to additional coordination of the Fe cations to the N-donors of the ligand. Finally, we introduce oxidation modulation – the concept of using metal precursors in a different oxidation state to that found in the final MOF – as a further protocol 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 capacity for the first time, suggesting that combining the two may be a powerful methodology for the controlled self-assembly of high-valent MOFs.<br><br>