A pure-culture Geobacter sulfurreducens microfluidic MFC with a membraneless configuration was used to study overshoot behaviour under controlled flow rates. Power overshoot was observed in the power density curves from a standard polarization test when applying different external resistors (from high to low) at cycle times of 1 to 2 hours. This drop is most likely related to a slow response from the microbes during adjustment to the new resistance. Eroding the outer EAB layers under strong shear forces improved the power density curve shape, but the overshoot at low Rext persisted. Moderate increases to the flow rate (below erosion levels) reduced overshoot, but its elimination could only be achieved via the in situ acclimation approach. No intervention made could cure the MFC from its unhealthy state (based on persistence of overshoot in the absence of acclimation, reduced cell voltage and lower current compared to the mature healthy state), but long-hold polarization tests produced results that were better than the results obtained using the standard polarization test applied to the healthy state. We anticipate that in situ acclimation could be applied to healthy MFCs for measurement results that are representative of long-term MFC operation. We conclude that the role of health state can cause challenges in properly conducting polarization test and that long-hold measurement are the best way to avoid artifacts such as overshoot in power density curves.