<p>There is a consistent increase in persistent organic pollutants and co-contaminants across diverse ecosystems. The polychlorinated biphenyls, polycyclic aromatic hydrocarbons and organochlorine pesticides along with heavy metals pose serious threats to our ecosystem and environment. Use of conventional physical and chemical decontamination technologies of persistent organic pollutant removal is often discouraged due to their operational complexities and potential environmental hazards. The pollutant removing potential of certain plants has been attributed to the assemblance of putative microbial populations residing in their inner tissues, popularly known as the endophytes. The current review addresses the potential of endophyte microbial mutualists as significant contributors in phytoremediation. The intrinsic metabolic machineries of the endophytic fungal cell factories accelerate the host plant’s mechanism in pollutant decontamination. Notwithstanding significant progress in the field, a comprehensive understanding of host-endophyte interaction during pollutant removal is still challenging. In this context, the current review has been designed to study the mechanistic interactions of endophyte fungi-mediated phytoremediation of persistent organic pollutants and co-contaminants. The review delineates the characteristics of various persistent organic pollutants, provides a concise overview of endophytic and arbuscular mycorrhizal fungi, and elucidates their essential mechanisms in augmenting the phytoremediation of persistent organic pollutants and associated contaminants. The recent update discusses technological interventions in host-fungal endophyte interactions that enhance phytoremediation efficiency and highlights potential in future research approaches.</p>