Salts of phosphonic acid (sodium or potassium phosphonate) or its ester fosetyl are highly effective systemic fungicides, which not only exhibit fungistatic activities, but also stimulate the natural defence systems of the plants against pathogens. Since EU legislation has approved potassium and sodium phosphonate as fungicides in 2013 and 2014, they are no longer permitted in organic agriculture. As a result, even minor contents of phosphonate in organic food samples are interpreted as an indication of a not permitted fungicide treatment. A maximum level of 0.01 mg/kg applies for food for infant nutrition. Here we present evidence from the scientific literature that phosphonate is also a natural compound, which occurs in significant amounts in the environment and is produced and consumed by microorganisms within the biogeochemical phosphorus cycle. Further potential sources for this chemical in the environment apart from agricultural fungicide applications are organophosphonates, as phosphonate occurs as a byproduct during their industrial production or during their microbial degradation in effluents from industry and households. An evaluation of Eurofins results from the analysis of phosphonate from 2017 to 2022 with methods achieving a limit of quantification (LOQ) of 0.01 mg/kg reveals that the compound was detected in 40.63% of all samples from organic and 43.42% from conventional agriculture, and in over 90% of organic samples of chickpeas, lentils, buckwheat, peanuts and wine. Furthermore, 97.3% of organic mushroom samples contain the compound and animal manure or compost used for cultivation is a potential source of the chemical. Consequently, other causes for phosphonate in food products than fungicide applications must be taken into account as well. Analysis of the ratio of the stable oxygen isotopes 18O and 16O was successfully applied to detect applications of mineral sulphur fertilizer in organic agriculture. Similarly, it might be also a promising tool to differentiate between phosphonate produced industrially and from natural sources.