The peralkaline Ilímaussaq Intrusion of the Gardar Province in South Greenland consists of several intrusive phases that have been related to different magmatic pulses and igneous cumulate processes. The lowermost exposed part of the intrusion is kakortokite, a eudialyte‐nepheline syenite, with distinctive sub‐horizontal layering which passes upwards into lujavrite, a fine‐grained melanocratic eudialyte‐nepheline syenite. Along the contact between kakortokite and lujavrite lies a transitional layered kakortokite, which has been defined previously based on textural and mineralogical criteria. However, published literature presents conflicting descriptions of this sequence in terms of thickness, layering, contacts, and mode of origin. Our own and previous field and petrographic investigations suggest that parts of the eudialyte‐rich zones in the transitional layered kakortokite comprise metasomatized and partially assimilated naujaite autoliths, a sodalite‐rich eudialyte nepheline syenite, detached probably from the roof of the intrusion. Here, we focus on the nature of the transitional layered kakortokite and conclude, in contrast to the conventional model, that it was formed by metasomatic transformation and assimilation of naujaite autoliths. We propose that the breakdown and replacement of sodalite locally increased chlorine and sodium concentrations, which may have catalyzed the precipitation of eudialyte. In detail, we suggest that the uppermost four eudialyte‐rich horizons were strongly influenced by metasomatic processes caused by mineral‐melt reaction, and were not simply the result of conventional igneous magmatic cumulate formation, as has been inferred for the underlying kakortokite layered units. Recognition of a significant metasomatic process has important bearing on the distribution of minerals with specific elements, like REE in eudialyte, both from a petrological and an economic perspective.