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.