Organic bananas for export are commonly protected against crown rot using formulations containing grapefruit seed extracts (GSEs). The production process and chemical composition of these GSEs are unclear; however, various formulations have been found to be compatible with organic agriculture standards as ‘plant preparations’ by organic certification bodies. In mid-2012, widespread contamination of bananas involving quaternary ammonium compounds (QACs), notably benzalkonium chloride (BAC) and didecyl dimethyl ammonium chloride (DDAC) was detected and could evidently be attributed to GSE formulations containing these compounds. The author reports the results of chemical analyses of commercial export consignments of organic bananas from Peru and Ecuador and pineapples from Costa Rica. These consignments were treated with approved commercial GSE-based organic post-harvest formulations. Analyses were conducted within the scope of a commercial residue screening programme. Results indicated frequent contamination of fruits with QACs. Chemical analysis of pure GSE-based post-harvest formulations showed widespread contamination with QACs, proving that these formulations cause QAC contamination in fruits. In vitro testing of the antimicrobial action of GSE-based formulations indicates that their efficacy is essentially due to QACs, which is confirmed in the previous literature. Because no credible chemical pathway for natural formation of QACs during extraction from grapefruit seeds has been found, QACs are considered as chemical contaminants. Certification bodies must be careful while evaluating the equivalence of such products to the standards of organic agriculture. Thorough information about the nature, origin, production process and chemical composition is needed in addition to scientific evidence of efficacy in the equivalence declaration process to avoid fraud.