The detection and quantification of Cs+ in aquatic media are an environmental safety and public health matter, so far limited by the lack of rapid, low cost, low limit of detection and selective analytical tools. Herein we demonstrate the efficient fabrication of a novel electrolyte-gated organic field-effect transistor sensor for the Cs+ detection in seawater based on the combination of two ultra-thin layers namely poly(3-hexylthiophene) as semiconductor and a single lipids monolayer as dielectric. The latter is end-capped with a specific Cs+ probe based on a calix[4]arene benzocrown ether to ensure the selectivity. Interestingly, we clearly evidence that by controlling affinity driven guest/host ion exchange, one can lift the general problem of selectivity encountered in all FET-based ion sensors, reaching a nearly perfect selectivity even in highly complex analyte solutions containing competitive ions, such as phosphate buffered saline solution or seawater. Such ultra-thin transistor structure exhibits, a limit of detection at the sub-femtomolar level which corresponds to a 5 folds’ magnitude lower than Inductively Coupled Plasma Mass Spectroscopy, the most commonly used technic today. These results pave the way to a generalized monitoring of Cs+ in complexed analytes.