To better understand muscle bioenergetic regulation, a previously‐developed model of the skeletal muscle cell bioenergetic system was used to simulate the influence of: 1) each step activation (ESA) of NADH supply (including glycolysis) and oxidative phosphorylation (OXPHOS) complexes; and 2) glycolytic inhibition by protons, on the kinetics of ATP synthesis from OXPHOS, anaerobic glycolysis and creatine kinase (CK). Simulations were fitted to previously published experimental data of ATP production fluxes and metabolite concentrations during moderate and severe intensity exercise transitions in bilateral knee‐extension in humans. Overall, computer simulations agreed well with experimental results. Specifically, a large (>5‐fold) direct activation of all OXPHOS complexes was required to simulate measured phosphocreatine (PCr) and OXPHOS responses to both moderate and severe intensity exercise. In addition, slow decay of ESA was required to fit PCr recovery kinetics, and the time constant of ESA decay was slower following severe (180 s) than moderate (90 s) exercise. Additionally, a strong inhibition of (anaerobic) glycolysis by protons (glycolytic rate inversely proportional to the cube of proton concentration) provided the best fit to the experimental pH kinetics, and may contribute to the progressive increase in oxidative ATP supply during acidifying contractions. During severe‐intensity exercise an ‘additional’ ATP usage (a 27% increase at 8 min, above the initial ATP supply) was necessary to explain the observed VO2 slow component. Thus parallel activation of ATP usage and ATP supply (ESA), and a strong inhibition of ATP supply by anaerobic glycolysis, were necessary to simulate the kinetics of muscle bioenergetics observed in humans. This article is protected by copyright. All rights reserved