This paper describes the design and operation of power conditioning system with maximum power transfer tracking (MPTT) for low-power electromagnetic energy harvesters. The system is fully autonomous, starts up from zero stored energy, and actively rectifies and boosts the harvester voltage. The power conditioning system is able to operate the harvester at the maximum power point against varying excitation and load conditions, resulting in significantly increased power generation when the load current waveform has a high peak-to-mean ratio. First, the paper sets out the argument for MPTT, alongside the discussion on the dynamic effects of varying electrical damping on the mechanical structure. With sources featuring stored energy, such as a resonant harvester, maximum power point control can become unstable in certain conditions, and thus, a method to determine the maximum rate of change of electrical damping is presented. The complete power conditioning circuit is tested with an electromagnetic energy harvester that generates 600 mV rm s ac output at 870 μW under optimum load conditions, at 3.75 m·s −2 excitation. The digital MPTT control circuit is shown to successfully track the optimum operating conditions, responding to changes in both excitation and the load conditions. At 2 V d c output, the total current consumption of the combined ancillary and control circuits is just 22 μA. The power conditioning system is capable of transferring up to 70% of the potentially extractable power to the energy storage.