Microbial fuel cells (MFCs) are sources harvesting energy from organic matters and showing great promise in powering environmental sensors. Because of the low power and voltage issues (100µW at 0.3V for 20 cm² electrodes), an electrical interface is required to extract the maximum power delivered by the MFC and boost the output voltage. However the switching operation of most converters induces a pulsed sinking current which may cause additional dynamic losses inside the MFC. Following a previous study on a flyback converter in discontinuous conduction mode, this paper analyzes the effect of switching of the converter on the MFC internal losses. A dynamic model of the MFC is deduced from an impedance spectroscopy characterization: it reveals a double RC behavior, one with a time constant of 10s of s, the other one of 100s of µs. Then in the frequency-domain, the MFC dynamic losses, induced by a previously optimized flyback, are calculated: they represent 50% of the maximum power that can be extracted from the MFC. Eventually in order to reduce these losses, we study the impact of three flyback parameters (primary inductance, duty cycle and decoupling capacitance). Adding a capacitance of 10 µF at the converter input, the MFC dynamic losses become negligible.