Organic farming for higher ecological and human health benefits has been adopted in about 186 countries, covering a total area of 71.5 Mha worldwide. Because of the associated practices, the flows of several environmental pollutants into the organic products threaten food safety and human health. The contaminants that occur at higher concentrations in organic produce include persistent organic pollutants (61.3-436.9 ng g lamb meat, and 0.28 pg g-2.75 ng g bovine meat), heavy metals (0.5-33.0 mg kg lettuce), organochlorine pesticides (11-199 μg g carrots), cyclodienes, hexachlorocyclohexanes, hexabromocyclododecane (2-3 times higher than in conventionally produced porcine meat), hexachlorobenzene (1.38-14.49 ng g fat in milk), and non-brominated flame retardants (1.3-3.2 times higher than in conventional produce of greenhouse-grown tomato and cucumber). Moreover, some pollutants like per- and polyfluoroalkyl substances with a longer half-life (1.50-9.10 yrs) are reported to occur in several organic products. In fact, several legacy persistent organic pollutants are known for their significant trophic magnification in an urban terrestrial ecosystem. In addition, many plant functionalities are adversely affected in organic farming. Therefore, the long-term usage of organic products containing such pollutants poses a significant threat to human health. The major limitation in organic livestock production is the severe shortage of organic feed. Several variable standards and technical regulations set by the government and private agencies are the major obstacles in the global marketing of organic products. The present review critically addresses the impact of organic farming on hidden risks due to the use of composts as the amendment resources that enhance the phytoaccumulation and trophic transfer of pollutants, the functional diversity of the ecosystems, and poor harmonization among the policies and regulations in different countries for organic farming. The future directions of research have been suggested to mitigate unintended flows of pollutants into the organic products.