Sediment microbial fuel cells (SMFCs) are energy harvesting devices where the anode is buried inside marine sediment, while the cathode stays in an aerobic environment on the surface of the water. To apply this SCMFC as a power source, it is crucial to have an efficient power management system, leading to development of an effective energy harvesting technique suitable for such biological devices. In this work, we demonstrate an effective method to improve power extraction with SMFCs based on anodes alternation. We have altered the setup of a traditional SMFC to include two anodes working with the same cathode. This setup is compared with a traditional setup (control) and a setup that undergoes intermittent energy harvesting, establishing the improvement of energy collection using the anodes alternation technique. Control SMFC produced an average power density of 6.3 mW/m2 and SMFC operating intermittently produced 8.1 mW/m2. On the other hand, SMFC operating using the anodes alternation technique produced an average power density of 23.5 mW/m2. These results indicate the utility of the proposed anodes alternation method over both the control and intermittent energy harvesting techniques. The Anode Alternation can also be viewed as an advancement of the intermittent energy harvesting method.