The synthesis of chemically stable metal–organic frameworks (MOFs) in benign solvents is a key step towards their scalable production and commercialization. Extending the modulated hydrothermal (MHT) synthesis approach for zirconium (Zr) MOFs, we herein demonstrate cluster nuclearity control over the secondary building units (SBUs) to target Zr₆-based and Zr₁₂-based phases for the Zr terephthalate (Zr-BDC) system. Different functional groups (–NH₂, –NO₂, –Br, –F₄) can be incorporated into Zr₁₂-BDC, providing an avenue to further tune the chemical properties of these promising MOFs.