Bariatric surgery may induce protein malabsorption, although data are scarce. This study aims at evaluating dietary protein bioavailability after different bariatric surgeries in rats. Diet-induced obese Wistar rats were operated for vertical sleeve gastrectomy (VSG) or Roux-en-Y gastric bypass (RYGB). The control group was composed of pair-fed, sham-operated rats (Sham). Two weeks after surgery, rats were fed a 15N protein meal. Protein bioavailability was assessed by determination of 15N recovery in the gastrointestinal tract and organs 6 h after the meal. Fractional protein synthesis rate (FSR) was assessed using a flooding dose of 13C valine. Weight loss was the highest in RYGB rats and the lowest in Sham rats. Surprisingly, RYGB (95.6 ± 0.7%) improved protein digestibility (P = 0.045) compared with Sham (93.5 ± 0.5%) and VSG (93.8 ± 0.6%). In contrast, 15N retained in the liver (P = 0.001) and plasma protein (P = 0.037) was lower than in Sham, with a similar trend in muscle (P = 0.052). FSR was little altered by bariatric surgery, except for a decrease in the kidney of RYGB (P = 0.02). The 15N distribution along the small intestinal tissue suggests that dietary nitrogen was considerably retained in the remodeled mucosa of RYGB compared with Sham. This study revealed that in contrast to VSG, RYGB slightly improved protein digestibility but altered peripheral protein bioavailability. This effect may be ascribed to a higher uptake of dietary amino acids by the remodeled intestine.NEW & NOTEWORTHY Using a sensitive 15N meal test, we found that gastric bypass slightly improved protein digestibility compared with sleeve gastrectomy or control but, in contrast, lowered protein retention in the liver and muscles. This paradox can be due to a higher uptake of dietary nitrogen by the intestinal mucosa that was hypertrophied. This study provides new insight on the digestive and metabolic fate of dietary protein in different models of bariatric surgery in rats.