In endodontic (root canal) treatment, a multispecies bacterial and fungal infection is present in a place that is inaccessible to the host immune system and which offers physical protection from applied topical agents. All current protocols for irrigation suffer various deficits in performance, which is why further research on alternative approaches to using antimicrobial substances is warranted. This chapter examines the technical and clinical factors which influence the performance of antimicrobial biocide-based therapies used in endodontics within dental practice, addressing issues around instability of biocides, the influence of pH, the role of physical agitation and the challenge of penetration into biofilms and into confined spaces. A range of methods to overcome the challenges in performance are described, including novel solvents and vehicles for biocides, stabilizing agents, physical agitation and the use of activation protocols including the use of intense light, ultrasound and laser-generated shockwaves to improve the effect of biocides. While specific examples are given from the dental setting of endodontics, the principles have broader application to medicine and to general industry.