Acid modulation is among the most widely employed methods for preparing metal–organic frameworks (MOFs) that are both stable and highly crystalline, yet there exist few guiding principles for selecting the optimal modulator for a given system. Using the Zr-based MOFs UiO-66 and UiO-68-Me2 (UiO = Universitetet i Oslo) as representative materials, here we present for the first time an in-depth structure–activity study of acid modulators and identify key principles of modulation for the synthesis of highly crystalline Zr-MOFs. By applying whole pattern fitting of powder X-ray diffraction patterns as a technique for evaluating modulator efficacy, complemented by scanning electron microscopy, 1H NMR, and thermogravimetric analysis (TGA), we demonstrate that the key to effective modulation is competition between the linker and modulator for coordination to the Zr secondary building units (SBUs). Specifically, we illustrate that a close match in pK a and structure between the linker and modulator favors larger and more well-defined crystallites, particularly with sterically unhindered aromatic acid modulators. Based on our findings, we demonstrate that 5-membered heteroaromatic carboxylic acids are among the most efficient acid modulators identified to date for the synthesis of several representative Zr-MOFs with fcu net topologies. In addition, we find that coordination modulation is superior to exogenous acid modulation at higher modulator concentrations. Finally, we compare 1H NMR and TGA as data-driven methods for quantifying linker deficiencies in modulated MOF syntheses. The guiding principles established herein have critical implications for the scalable and controllable synthesis of highly crystalline and stable MOFs relevant to chemical separations, gas storage, and catalysis.