This Feature Article focuses on recent progress made in elucidating the intermolecular interactions between a novel class of synthetic phenylene ethynylene (PPE)-based conjugated polyelectrolyte polymers (CPEs) and oligomers (OPEs) and multiscale cellular targets that give rise to their remarkable broad spectrum biocidal activity. We first review the interactions and self-assembly behaviors of the CPEs and OPEs with a set of vital biomolecules, including lipids, proteins, and nucleic acids, that reveal the potential pathways by which synthetic biocidal agents could exert toxicity. An overview of the antimicrobial effects and mechanisms of the CPEs and OPEs on multiple clinically relevant pathogens is then presented, with an emphasis on the morphological damage induced by the biocidal compounds toward the pathogens. Finally, we discuss the cytotoxicity of these materials against mammalian cells and human tissues to explore the potential applications of the CPEs and OPEs as antiseptics. We also pose some unanswered questions about their antimicrobial mechanisms, which provide direction for a future study.