The microbial desalination cell (MDC) is a promising technology to desalinate water without electrical energy input. In this study we developed a new configuration of an MDC called a microbial electrodeionization cell (MEDIC) stack using an MDC packed with ion-exchange resins (IERs) to enhance water desalination. Two different volumes (1.5 mL and 2.5 mL) of IERs were tested and compared to a control MDC without resins. The MEDIC reactor with 2.5 mL IER improved desalination performance by ~ 40% using a relatively low-concentration salt solution and produced better quality water than the control MDC, due to the decrease in ohmic resistance by almost 28 Ω and improved cell conductivity. With 2.5 mL of IERs, power density increased by 70% from 0.38 (control MDC) to 0.65 W/m2.These results demonstrated that substantially improved performance can be achieved with an MEDIC reactor compared to conventional MDCs due to the use of IERs.