This study explores photobiomodulation (PBM) effects on isolated mitochondria from a thermodynamic perspective, focusing on energy transfer processes. The research reveals significant findings on the energy absorbed and biochemical energy produced by mitochondria when exposed to specific laser parameters. The study shows measurable energy conversion efficiencies, highlighting the potential of PBM in mitochondrial applications. The results indicate that PBM efficiency is non-negligible, surpassing the energy conversion rates seen in green plants' photosynthesis. However, uncertainties remain, especially in energy estimates and biological variability, pointing to the complexity of these processes. The study also challenges the principle of irradiance reciprocity, showing that PBM effects do not solely depend on fluence, suggesting substantial deviations from established photobiological laws. These findings are the first of their kind in PBM research on isolated mitochondria and open new avenues for understanding light-matter interactions at the cellular level.