Jiaxu, Christopher and coauthors show that well-defined, hydrogen-terminated molecular nanographenes serve as chemically confined precursors for high-pressure, high-temperature synthesis of ultrasmall (3–4 nm), monodisperse and highly crystalline molecular nanodiamonds (m-NDs) with only a single sp² surface reconstruction and produced on a milligram scale, establish a scalable and modular route to high-quality molecular and fluorescent nanodiamonds and offer a general design principle for tailored quantum materials and nanoscale devices.