With a presence of the Wood-Ljungdahl pathway, acetogenic bacteria are capable of converting C1 feedstocks into biomass and various metabolites, receiving industrial interest in microbial production of biochemicals derived from C1 substrates. To understand C1 feedstock fermentation using acetogenic bacteria, most of the studies have focused on revealing their carbon assimilation and energy conservation systems. Despite the determination of the essential mechanisms, a fundamental understanding of acetogenic bacteria and the associated complex regulatory systems remains unclear and is needed for rational strain design. For this purpose, systems biology is a suitable approach for investigating genome, transcription, translation, regulation systems, and metabolic flux, providing a glimpse of the relationship between the genotype and phenotype of the organisms. This chapter will cover recent systems biology applications on acetogenic bacteria and discuss the cellular responses during C1 feedstock fermentation along with the regulatory systems that orchestrate cellular processes.