A critical survey concerning biocidal energetics is proposed according to a classification depending on their chemical structure. The need of optimizing the performances of such compounds is an important target for the inertization of biological weapons, requiring a synergy between the thermal effects of combustion/detonation with the biocidal effects of reaction products released into the environment. The main physicochemical aspects related to the synthesis technique, the thermodynamic variables and the antimicrobial activity have been discussed and compared. In particular, different kinds of biocides have been taken into account, with particular attention to the role of iodine as one of the most promising and eco-friendly chemical species to this purpose, in line with the paradigms of environmental protection and the rational utilization of chemicals. Furthermore, the protocols adopted to assess the effectiveness of biocidal agents have been thoroughly examined according to the recent studies proposed by some of the most reputable research groups in the field. Finally, some insights for future investigations are proposed.