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The rare alkali ion caesium (Cs+) is assimilated by eukaryotes, even though it is not an essential nutrient. It poses an environmental concern through the anthropogenic release of its radioisotopes, 134Cs and 137Cs. Bioavailability and long half-lives favour its uptake and accumulation in plants, via which radiocaesium can be introduced to the food chain. Cs+ ions are taken up via potassium-(K+)-related pathways due to the biophysical similarity of these cations. This makes it difficult to solely manipulate Cs+ accumulation in plants without disturbing the homeostasis of essential ions at the same time. This work shows that the soluble N-ethylmaleimide sensitive factor attachment receptor (SNARE) Sec22p, previously described as a member of the protein sorting machinery, specifically affects Cs+ accumulation in yeast by regulating the selectivity of vacuolar deposition. A similar phenotype became apparent for a homologous plant protein, SEC22. The loss of Saccharomyces cerevisiae Sec22p reduces Cs+ uptake by more than half, while at the same time leaving essential cations undisturbed. Mathematical modelling of wild-type and mutant Cs+ uptake kinetics proposes that sec22Δ is defective in vacuolar compartmentalisation of Cs+, which is proven by biochemical fractionation. Morphological alterations were not produced by the loss of Sec22p, only a Cs+-dependent vacuolar fragmentation can be observed. These results indicate a so far undescribed function of Sec22p in assuring a non-selective ion deposition to the vacuole, which is necessary in ion detoxification, while its loss induces discrimination against vacuolar Cs+ deposition. A developmentally controlled loss-of-function mutant of the orthologous gene SEC22 (At1g11890) in A. thaliana displays a similar phenotype, having specifically reduced Cs+ enrichment without detrimental growth defects, thereby translating the yeast findings to a multicellular context. Furthermore, a functional complementation of the yeast mutant Cs+ phenotype by the plant gene transcript was possible. Selective reduction of Cs+ accumulation in plants by loss of a single gene product represents a new route to limit radiocaesium input to the food chain without disturbing basic plant nutrition and growth.