Nucleation processes in wet-chemical synthesis methods are poorly understood, nevertheless an atomistic understanding of material formation would aid in the design of synthesis methods for tailor-made functional materials. Here, in situ X-ray total scattering experiments were performed during the hydrothermal synthesis of wolframite-type MWO4 (M: Mn, Fe, Co, Ni), enabling pair distribution function (PDF) analysis of the process. Upon mixing of the aqueous precursors, a crystalline precursor formed for the MnWO4 synthesis, while amorphous pastes formed for the FeWO4, CoWO4 and NiWO4 syntheses. Upon heating, the crystalline MnWO4 precursor converted directly to a crystalline wolframite-type MnWO4 phase, while the amorphous precursor led to the formation of an intermediate phase before the crystalline tungstates. The structure of the amorphous precursors was studied in detail using PDF analysis. Database mining was initially used to extract chemically relevant cluster structures, with the conclusion that the structure of the precursor contains Keggin fragments, well known from polyoxometalate chemistry. Such fragments are present in the Tourné ‘sandwich’ cluster, which has previously been found to be involved in the formation of some tungstates. We then used our recently developed ML-MotEx algorithm to identify which structural motifs in the sandwich structure are important to obtain a good fit of the data throughout the reaction. This analysis led to the identification of a skewed sandwich cluster to best describe the amorphous precursor structures. For the intermediate phase, ML-MotEx favoured motifs found both in the precursor and product phases, and the PDF of the intermediate phase could be described up to 20 Å by a disordered MWO4 structure. We found that the more disordered the precursor phase is, the longer reaction time is required to form crystalline products. More generally, we see that polyoxometalate chemistry is useful when describing the initial wet-chemical formation of mixed metal oxides.