Background Bariatric surgery (BS) is a very effective treatment regarding body weight loss but might affect food tolerance and energy and protein intake. The aim of this study was to compare three BS techniques (biliopancreactic diversion (BPD), gastric bypass (GB), and sleeve gastrectomy (SG)) and their effect on food tolerance. Methods Prospective study conducted between April 2016 and April 2019. Visits included were 1 before and 6, 12, and 24 months after BS. Food tolerance test (FTT), 24-h recall, and bioelectrical impedance (TANITA MC780) were performed at all visits. Results Sixty-six patients were included (74.2% women). FTT showed a better self-perception of the intake after surgery in BPD at 6 months ( p  = 0.013), and at 12 months ( p  = 0.006). BPD had a better tolerance of 8 food groups at 6 months (red meat p  = 0.017, white meat p  = 0.026, salad p  = 0.017, bread p  < 0.001, rice p  = 0.047, pasta p  = 0.014, fish p  = 0.027) and at 12 months, but only red meat ( p  = 0.002), bread ( p  < 0.001), rice ( p  = 0.025), and pasta ( p  = 0.025) remained statistically different. Twenty-four months after surgery, only the red meat food group ( p  = 0.007) showed differences. BPD had the lowest incidence of vomiting at 6 months ( p  < 0.001), 12 months ( p  = 0.008), and 24 months ( p  = 0.002). The total score of FTT was better in BPD at 6 months 25.6 (SD 1.5), p  < 0.001, 12 months 25.6 (SD 2.4), p  < 0.001, and 24 months 25.7 (SD 1.3), p  = 0.001. BPD showed the best intake in energy and proteins at 6 months 1214.8 (SD 342.4) kcal and 67.1 (SD 18.4) g and 12 months 1199.6 (SD 289.7) kcal and 73.5 (SD 24.3) g. % FML was higher in GB both at 6 and 12 months being statistically different ( p  < 0.050). Conclusion Biliopancreatic diversion appears to be the technique with a better food tolerance and protein and energy intake in the first year of follow-up after BS. Graphical Abstract