While pathogen-based bio-threats may be introduced to the water and food supply, the detection of pathogen-based bio-threats in air is particularly critical to biowarfare defense, as they may be introduced into the battlefield in the form of aerosols. Further, the dispersal of pathogen-based bio-threats by air in facilities (e.g., via air-handling systems) represents a significant domestic bioterrorism concern. Thus, biosensor-based assays for bio-threat applications should be low-cost and portable to enable integration with existing physical systems (e.g., facilities) and movement with the warfighter or drones on the battlefield. Having discussed transduction elements, biorecognition elements, electrochemical methods, measurement formats, and pathogen detection applications, we next discuss the present challenges and future directions in the field of electrochemical biosensor-based pathogen detection.