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For long duration scientific missions with stratospheric balloons (objective of 3 month duration), renewable energy is used. Solar panels with mono crystalline silicon solar cells are mounted on both scientific and avionic gondola. A power conditioning board with Maximum Power Point Tracking (MPPT) is designed and currently tested. This board is called MC2: Communicant Conditioning Module. It allows controlling a Li Ion battery charge through PWM regulators. Moreover, outlets ON/OFF commutations associated to overcurrent’s protections are implemented in this board. The battery active thermal control is made by MC2 autonomously. The main design drivers are mass, costs and efficiency. A CAN Bus between MC2 and On Board Computer allows to have a commandability and observability of MC2 through OBC. The overall avionic gondola is designed to be Single Points Failure free by using two segregated chains in order to be compatible with safety rules. The nominal chain is the main chain and use MC2 with renewable energy. The secondary chain uses a primary electrochemical cell which feeds loads in case of undervoltage of the main chain. This overall architecture allows both chains to be designed without SPF free constrains. This paper describes the overall requirements and the design of MC2. The main innovation described in this paper is the way to implement MPPT: the MPPT algorithm is performed at the output of the power converter. This MPPT extracts maximum power of both solar panel characteristics and power converter. The main advantage is that this MPPT uses only one existing sensor (output current of boost converter) instead of using current and voltage sensor of each solar panel.