Soil microorganisms metabolize the trace quantities of atmospheric hydrogen to persist in environments when nutrient sources are limited. High-affinity hydrogenases are the key enzymes that drive the oxidation of atmospheric H2. Although previous studies have indicated the importance of these hydrogenases in microbial persistence, the mechanism on how they function during carbon limitation is still unclear. In this work, we show how mycobacterial uptake hydrogenases Hup and Hhy are utilized and how they interact with the respiratory chain to generate energy during persistence. Gene expression and biochemical analyses revealed that the hydrogenases have differential expression profiles and activities. Although both hydrogenases are highly expressed and active upon carbon depletion, Hup is most upregulated and active in early-stationary while Hhy in mid- to late-stationary phase. In addition, both hydrogenases are membrane associated and solubilization experiments revealed that Hup forms a weak physical membrane association while Hhy is tightly bound to the membrane. This suggests that both hydrogenases interact with the electron transport chain during carbon limitation. This interaction is confirmed when respiratory chain uncouplers significantly decreased the H2 oxidation activities of Hup and Hhy. Respiratory measurements also revealed that electrons derived from the activities of both hydrogenases are fed into the quinone pool and are ultimately transferred to cytochrome bc1-aa3 complex. Interestingly, Hhy is also capable of terminally feeding the electrons to the cytochrome bd oxidase. From these findings, we present a model of how the mycobacterial hydrogenases are functionally linked to the respiratory chain during carbon starvation. The electrons derived from atmospheric H2 oxidation are used to maintain a membrane potential and support ATP generation via aerobic respiration. This has implications for how energy is conserved in oligotrophic environments, where microorganisms scavenge atmospheric trace gases to support microbial persistence.