The study aimed to verify the effect of intra- (beta-alanine—BA) versus extra- (alkaline agents—ALK) cellular buffering agent supplementation, combined with customarily used branched-chain amino acids (BCAAs) and creatine malate (TCM) treatment in natural training conditions. Thirty-one elite athletes (11 sprinters and 20 endurance athletes) participated in the study. Eight-week randomized double-blind, crossover, combined supplementation with BA-ALKplaBCAA&TCM and ALK-BAplaBCAA&TCM was implemented. In the course of the experiment, body composition, aerobic capacity, and selected blood markers were assayed. After BA-ALKplaBCAA&TCM supplementation, total fat-free mass increased in sprinters (p = 0.009). No other differences were found in body composition, respiratory parameters, aerobic capacity, blood lactate concentration, and hematological indices after BA-ALKplaBCAA&TCM/ALK-BAplaBCAA&TCM supplementation. The maximum post-exercise blood ammonia (NH3) concentration decreased in both groups after BA-ALKplaBCAA&TCM supplementation (endurance, p = 0.002; sprint, p < 0.0001). Also, lower NH3 concentrations were observed in endurance athletes in the post-exercise recovery period. The results of our study indicate that combined BCAA, TCM, and BA supplementation is more effective than combined BCAA, TCM and ALK supplementation for an increase in fat-free mass and exercise adaptation, but not for aerobic capacity improvement. Besides, it seems that specific exercise stimuli and the training status are key factors affecting exercise performance, even in athletes using efficient supplementation.