In this work, three double-compartment MFCs (DC-MFC) were operated for 1 month in order to compare their performances in terms of wastewater treatment capacity and electricity production and to get information about how this performance is influenced by the start-up procedure. To do this, they underwent different start-up procedures. One of them (aerobic-starved MFC) was inoculated with 100% fresh aerobic sludge, another (anaerobic-starved MFC) using 100% fresh anaerobic sludge, and finally a third one (aerobic-fed MFC) was inoculated using a mixture 10% fresh aerobic sludge and 90% synthetic wastewater (based on acetate). Then, from this start-up, the cells were operated exactly under the same feeding and operation conditions and they underwent the same tests. Results demonstrate that after one month of operation, in DC-MFCs, there are no significant differences in the steady state operation conditions reached because the three cells lead to a very similar treatment capacity, quantified in terms of the COD consumption rate, and to a quite similar value of the current produced. A comprehensive electrochemical characterization informed that the small differences cannot be explained in terms of the different start-up period. This means that the DC-MFC technology is robust enough regarding the inoculation and within systems undergoing the same disturbances, outputs obtained are quite the same, which becomes a very important observation for future works.