This work focuses on a computational investigation of the diffusion of substrates in the carbon monoxide dehydrogenase (CODH) and acetyl-coenzyme A synthase (ACS) enzymatic complex (CODH/ACS), which plays a central role in the Wood-Ljungdahl pathway for CO2 fixation. The CODH/ACS enzymatic complex catalyzes the (reversible) electrochemical conversion of CO2 to CO and the subsequent condensation of CO with a methyl intermediate and coenzyme A to form acetyl coenzyme A. CO2 reduction happens at the CODH C-cluster, and the CO product is transported and consumed at the ACS A-cluster. The bifunctionality of the complex is facilitated by a 140 Å-long gas channel for the transport of CO between the C- and A-clusters. A significant challenge in using the CODH/ACS complex for large-scale applications is its irreversible inactivation by O2, which could be mitigated by preventing the O2 gas from entering the enzyme complex. Here, we analyzed the gas channels between the A and C clusters and between the C clusters and the surface of the complex. Using a spherical probe to simulate CO and CO2, we determined a network of channels that became apparent during long-timescale molecular dynamics simulation. We then determined the free energetics of substrate diffusion in the dominant channels and identified potential barriers to substrate flow and O2 ingress. To this end, we have developed a new computational protocol to calculate the free energy of diffusion for CO2, CO, and O2 through the identified gas channels. We also identified potential bottlenecks (residues) that may hinder CO2 and O2 uptake and suggested restudies that can be mutated to facilitate selective CO2 uptake while preventing O2 from using the channels to affect inactivation. By understanding and modifying these diffusion pathways, we seek to enhance the efficiency and stability of CODH/ACS for future energy applications.