Implanted devices destined for contact with sterile body tissues, vasculature or fluids should be free of any microbial contamination that could lead to disease transmission. The disinfection and sterilisation of implantable biofuel cells is a challenging and largely overlooked subject due to the incompatibility of fragile biocatalytic components with classical treatments. Here we report the development of a convenient "soft" chemical treatment based on immersion of enzymatic bioelectrodes and biofuel cells in dilute aqueous chlorhexidine digluconate (CHx). We show that immersion treatment in a 0.5 % solution of CHx for 5 min is sufficient to remove 10-6 log colony forming units of Staphylococcus hominis after 26 h while shorter treatments are less effective. Treatments with 0.2 % CHx solutions were ineffective. Bioelectrocatalytic half-cell voltammetry revealed no loss in activity at the bioanode after the bactericidal treatment, while the cathode was less tolerant. A maximum power output loss of ca. 10 % for the glucose/O2 biofuel cell was observed following the 5 min CHx treatment, while the dialysis bag had a significant negative impact on the power output. Finally, we report a proof-of-concept in vivo operation for 4 days of a CHx-treated biofuel cell with a 3D printed holder and additional porous surgical tissue interface. Further assessments are necessary to rigorously validate sterilisation, biocompatibility and tissue response performance.