The aim was to evaluate pathogenic bacteria (PB) survival during the composting of chicken manure (CM) amended with five different dosages of clay compared to CM without clay-applied treatment. The results showed that 85-87% of PB relative abundances (RAs) were significantly reduced in lower dosages of applied clay (T2 and T3). However, the maximum survival of PB was noticed in the T6 and T5 treatments, but most of the PB belong to Firmicutes, Actinobacteria and Proteobacteria phylum and their derivative bacterial species. The changes in PB during the composting were not only strongly influenced by clay amendment but also significantly associated with the succession of bacterial species in compost. Bacillus, Clostridium, Mycobacterium and Klebsiella were the dominant spore-forming bacteria identified in higher dosages of clay (i.e., T4, T5 and T6) treatments, but very low abundance of these bacterial genus and its species were recovered from lower dosages of clay (T2 and T3)-applied treatments. Overall, without clay, amended-CM-derived compost contained a relatively higher PB abundance than other treatments, as the anaerobic bacterial species Clostridium_difficile_AA1, Vibrio_cholerae, and Acinetobactercalcoaceticus had relatively greater RAs, followed by Klebsiella_oxytoca_10-5248, Paenibacillus_Bacillus_cereus and Bartonella_quintana_RM-11. Thus, CM composting with 4% clay amendment is considered a useful method for the efficient recycling of CM, as this process produced sanitized compost with less survival of PB.