Decoding structural transitions during mechanochemical reactions remains challenging due to the transient and disordered nature of intermediate phases. In this study, we use a combination of in situ powder X-ray diffraction (PXRD) and terahertz (THz) Raman spectroscopy to investigate the amorphous-to-crystalline transformation that occurs during the formation of a metal–organic complex. The two probes complementary sensitivity reveals an amorphous intermediate preceding crystallisation, with water playing a pivotal role in activating the complexation process. Multivariate curve resolution (MCR) analysis enables the simultaneous interpretation of PXRD and Raman data, enhancing the detection of amorphous species and mapping their structural evolution in real time. This integrated approach provides a general framework for identifying disordered intermediates in mechanochemical synthesis.