Electrochemical aptamer-based (EAB) sensors encompass the only biosensor approach yet reported that is simultaneously: (1) independent of the chemical or enzymatic reactivity of its target, rendering it general; (2) continuous and real-time; and (3) selective enough to deploy in situ in the living body. Consistent with this, in vivo EAB sensors supporting the seconds-resolved, real-time measurement of multiple drugs and metabolites have been reported, suggesting the approach may prove of value in biomedical research and the diagnosis, treatment, and monitoring of disease. However, to apply these devices in long-duration animal models, much less in human patients, requires that they be free of any significant pathogen load. Thus motivated, here we have characterized the compatibility of EAB sensors with standard sterilization and high-level disinfection techniques. Doing so, we find that, while many lead to significant sensor degradation, treatment with CIDEX OPA (0.55% ortho-phthalaldehyde) leads to effective disinfection without causing any detectable loss in sensor performance.