The surface molecules of bacteria contribute significantly to the hosts response to both pathogens and commensals. However, the technology available to track these molecules in host cells and tissues remains primitive. To address this limitation, we have developed an expanded metabolic labeling approach that chemically tags lipopolysaccharide, capsular polysaccharide, and peptidoglycan simultaneously in live anaerobic commensal bacteria. This technology enabled us to track the entry of differentially labeled surface molecules from live, luminal bacteria into specific host intestinal immune cells and their subsequent degradation in host phagocytes. Notably, this approach also enabled live imaging of the tagged bacterial surface molecules from endogenous commensals in the intestine of the living murine host. These tools will make it possible for investigators to decipher the role of specific bacterial surface molecules in host response.