The intricate interplay between physical exercise, mitochondrial function, and lipid metabolism has garnered considerable attention, particularly in the context of energy balance and overall metabolic health. Studies comparing which exercise has the most beneficial effects on mitochondrial activity and lipid metabolism are still scarce. This study aimed to investigate the effects of anaerobic and aerobic exercise on mitochondrial activity and biogenesis, as well as lipid metabolism, in healthy young adults. Eighteen subjects (young male adults) were randomly divided into two groups: anaerobic exercise group (n=9) and aerobic exercise group (n=9) for 4 weeks. Blood samples were collected before and after training and the whole blood was separated into leucocyte cells and plasma. Lysate from leucocyte cells was used for the measurement of mitochondrial function, including succinate dehydrogenase (SDH) activity, peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α), and ATP levels. Blood plasma was used for the measurement of lipid metabolism, including HDL cholesterol, adiponectin, and free fatty acids levels. This study demonstrated that SDH activity increases significantly after aerobic exercise (122%) compared to before exercise, although it is not supported by the results of PGC-1a and ATP levels. This may be because these parameters are measured in the blood (leukocyte cells). Adiponectin levels increase significantly after anaerobic exercise (43.8%) while free fatty acid levels increase significantly after aerobic exercise (104%) compared to before exercise. The results of HDL cholesterol levels found a tendency to increase both after aerobic (12%) and anaerobic exercise (10%) compared to before exercise. We conclude that aerobic exercise gives the best impact on increasing mitochondrial activity systemically (significantly increasing SDH activity), supported by the significant increase in free fatty acid levels in the blood, which reflects that lipolysis is increased. Copyright: © 2026 by the author(s). Licensee Pandawa Institute, Metro, Indonesia. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).