Pegmatite-related deposits are among the most crucial sources of rare-metal elements such as Li, Be, Nb, Ta, Rb, Cs and Sn. Despite nearly 2 centuries of extensive study, the mechanism governing the rare-metal mineralisation of pegmatites remains contentious. Alongside the enrichment of rare-metal elements in the source region, differentiation processes after emplacement may have also contributed to the concentration and mineralisation of rare-metal elements. However, compared to fractional crystallisation, limited attention has been directed towards the role of liquid immiscibility in pegmatite mineralisation. In this study, the major and trace element compositions of garnets in the internally zoned (Be-rich) and un-zoned (barren) pegmatites from the Koktokay pegmatite field in Altai, NW China, were analysed to evaluate the role of liquid immiscibility in the generation of rare-metal mineralised pegmatites. The studied garnets belong to the almandine-spessartine solid solution and are magmatic in origin. The inter- and intra-crystal chemical variations observed for the studied garnets were produced by a combined effect of magmatic crystallisation and liquid immiscibility. The decrease in the spessartine component of garnets from the margins inward and the depleted MREE–HREE distribution patterns of garnet domains indicate the onset of liquid immiscibility, which correlates with the Be mineralisation of the internally zoned pegmatite. Therefore, the chemical variations in garnets from the Koktokay pegmatites suggest a clear genetic relationship between liquid immiscibility and rare-metal mineralisation, and they are proposed as potential indicators for prospecting rare-metal ore deposits.