Background/Objectives: Bariatric surgery candidates require presurgical physical training, therefore, we compared the metabolic effects of a constant moderate-intensity training program (MICT) vs. a high-intensity interval training (HIIT) in this population. Methods: Seventeen participants performed MICT (n = 9, intensity of 50% of heart rate reserve (HRR) and/or 4-5/10 subjective sensation of effort (SSE)) or HIIT (n = 8, 6 cycles of 2.5 min at 80% of the HRR and/or 7-8/10 of SSE, interspersed by 6 cycles of active rest at 20% of the FCR) for 10 sessions for 4 weeks. After training, tissue samples (skeletal muscle, adipose tissue, and liver) were extracted, and protein levels of adiponectin, GLUT4, PGC1 alpha, phospho-AMPK/AMPK, collagen 1 and TGF beta 1 were measured. Results: Participants who performed MICT showed higher protein levels of PGC-1 alpha in skeletal muscle samples (1.1 +/- 0.27 vs. 0.7 +/- 0.4-fold change, p < 0.05). In the liver samples of the people who performed HIIT, lower protein levels of phospho-AMPK/AMPK (1.0 +/- 0.37 vs. 0.52 +/- 0.22-fold change), PGC-1 alpha (1.0 +/- 0.18 vs. 0.69 +/- 0.15-fold change), and collagen 1 (1.0 +/- 0.26 vs. 0.59 +/- 0.28-fold change) were observed (all p < 0.05). In subcutaneous adipose tissue, higher adiponectin levels were found only after HIIT training (1.1 +/- 0.48 vs. 1.9 +/- 0.69-fold change, p < 0.05). Conclusions: Our results show that both MICT and HIIT confer metabolic benefits in candidates undergoing bariatric surgery; however, most of these benefits have a program-specific fashion. Future studies should aim to elucidate the mechanisms behind these differences.