Abstract The green and cost-effective nature of the microbial desalination cell (MDC) make it a promising alternative for future sustainable desalination. However, MDC suffers from a low desalination rate that inhibits it being commercialized. External resistance (Rext) is one of the factors that significantly affect the desalination rate in MDCs, which is still under debate. This research, for the first time, investigated the impact of Rext on MDCs with different internal resistance (Rint) of the system to discover the optimal range of Rext for efficient MDC performance. The results showed that the effect of Rext on desalination rate (2.52 mg/h) was quite low when the Rint of MDC was high (200 Ω). However, operating the MDC with a low Rint (67 Ω) significantly improved the desalination rate (9.85 mg/h) and current generation. When MDC was operated with a low Rint the effect of variable Rext on desalination and current generation was noticeable. Therefore, low Rint (67 Ω) MDC was used to select the optimum Rext when the optimal range was found to be Rext ≪ Rint, Rext < Rint, Rext ≈ Rint (ranging from 1–69 Ω) to achieve the highest desalination rates (10.41–8.59 mg/h). The results showed the superior effect of Rint on desalination rate before selecting the optimal range of Rext in the outer circuit.