Chemical sanitisers are needed for controlling microbial contamination and growth in various settings, including healthcare, domestic settings and the food industry. One promising sanitiser with proposed applications in the food industry is the oxidising sanitiser electrolysed water (EW). For EW applications to be effective, a more in-depth understanding of EW mode-of-action is needed, together with the identification of limiting factors associated with the chemical matrices in relevant EW applications. This study investigated the reactivity of EW with different organic substances. For this purpose, the common food spoilage fungus Aspergillus niger was treated with EW in the presence or absence of the organic materials. The sanitiser retained partial fungicidal activity at high levels of added soil, commonly associated with freshly harvested produce. By narrowing down the reactivity of EW from complex matrices to specific organic molecules, proteins and amino acids were found to strongly suppress EW fungicidal activity. The potential implications of EW reactivity with proteins and amino acids within cells were investigated in the fungal model organism Saccharomyces cerevisiae. This capitalised on the advanced understanding of the uptake and metabolism of diverse compounds and the availability of convenient genetic tools in this model organism. Pre-culture with methionine but not with other tested amino acids increased yeast resistance to subsequent treatments (in the absence of methionine) with sanitisers (EW, sodium hypochlorite, ozonated water). Further tests suggested a direct role of the methionine molecule itself, as opposed to downstream products of methionine metabolism or methionine misincorporation in proteins, in increasing yeast EW resistance. Intracellular methionine oxidation can disturb FeS cluster proteins and this study found that EW treatment impairs FeS cluster protein activity. Because active species in EW can be inactivated by organic compounds, microorganisms may be exposed to low effective EW doses during EW treatments where organic matter is present. When low, sub-lethal EW doses were applied to A. niger, early germination events and colony growth post-treatment were delayed and there was increased variation in size among resultant colonies. The delay and increased variation were non-heritable and were observed with chlorine-containing sanitisers (EW, sodium hypochlorite) but not the chlorine-free oxidant ozonated water. The collective findings led to a hypothesis that chloramine formation within spores during EW treatment may contribute to the observed phenotypes. This study increases the understanding of limiting chemical factors for EW applications and sheds light onto the cellular mode-of-action of EW and the fungal response mechanisms to sanitiser treatments. Such insights can improve the rational development of EW application processes and contribute to understanding and prediction of antimicrobial efficacy in diverse settings.