Germanium has emerged as a promising high-capacity anode material for lithium ion batteries. To understand the microstructure evolution of germanium under different cycling rates, we monitored single germanium particle batteries using an in situ focused ion beam-scanning electron microscope. Our results show that both the lithium concentration and delithiation rate have an impact on nanopore formation. This study reveals that germanium electrodes with low and high cycling rates have better microstructure integrity, which leads to better cycling performance. The nanopores tend to aggregate into large porous structures during cycling which leads to particle pulverization and capacity fading of the electrode.