In this work, a microfluidic MFC with a pure-culture G. sulfurreducens was observed while it transitioned from a healthy to an overshooting state. We conducted a quantitative analysis of the degree of overshoot following the application of different flow rates, including those high enough to cause shear erosion of the outer biofilm layers. EAB erosion cured some, but not all, of the anomalies in the power density curve. Pre-acclimation to low external resistances before standard polarization tests resulted in maximum power density measurements that matched those of the healthy MFC (before displaying overshoot) but the maximum current density was still reduced. Finally, a new microfluidic-assisted long-hold polarization test for in situ acclimation at all external resistances improved the measured maximum power and maximum current densities, even beyond those made on the healthy EAB using a standard polarization test measurement. This approach shows promise for accurate studies of the influence of the polarization test parameters on the measured results and points to the fundamental importance in making measurements on EABs that have attained long-term stability.