The Swachh Bharat Mission was launched by the Prime Minister of India in 2014 with the objective of achieving the status of an open-defecation-free (ODF) country. The Mission was deemed successful when India declared itself open-defecation-free (ODF) in 2019. The country is now focusing on achieving ODF+ status that includes ensuring the sustainability of the ODF status, as well as the ODF++ status that ensures safe collection, conveyance, treatment and disposal of all faecal sludge and sewage in the country. Keeping this in mind, many faecal sludge treatment plants (FSTPs) have been constructed or are under construction in the country. The FSTPs are constructed for treating faecal sludge and septage (FS&S) that is generated from the onsite sanitation systems namely, septic tanks and pit latrines. A performance evaluation of FSTPS conducted by CSE shows that the liquid effluent generated from several FSTPs is non-compliant with existing Indian regulations (MoEF&CC, 2017) for COD, TKN and faecal coliform. It was observed that the solid residue generated from many FSTPs is high in pathogen content. Keeping this in consideration, the current report focuses on the reduction of pathogens in FSTPs by providing operational guidelines and best practices for the efficient use of treatment technologies so that the FSTP effluents/products are safe for reuse or disposal.