Feed efficiency in salmonids depends on intestinal capacity to adapt to dietary changes. Intestinal SLC transporters involved in amino acid uptake are key components of adaptation to alternative aquafeed ingredients. Brewer’s spent grain (BSG) is a sustainable ingredient, but fiber and antinutritional factors limit nutrient bioaccessibility. Mycelial fermentation may improve nutrient availability and add bioactive compounds like ergothioneine. Juvenile rainbow trout were fed control, BSG, or BSG fermented by the fungus Pleurotus ostreatus (BSGPO) diets for 28 days. Gene expression was analyzed in pyloric caeca, mid-intestine, and distal intestine (n = 3 biological replicates), including SLC transporters, brush-border peptidases (lpep, anpep), alkaline phosphatase (alp), and the ergothioneine transporter (EGTT). In the distal intestine, the BSGPO diet increased expression of the brush-border peptidases lpep (11.5-fold, P = 0.013) and anpep (28.3-fold, P = 0.037), the neutral amino acid transporter slc1a5 (5.9-fold, P = 0.044), cationic amino acid transporters slc3a1 (71.8-fold, P < 0.001) and slc7a3 (12.8-fold, P = 0.029), and EGTT (15.0-fold, P = 0.008). Additionally, both BSG-based diets upregulated the neutral amino acid transporter slc43a1 (5.7- and 5.9-fold; P = 0.047 and 0.048), whereas only BSG increased the basolateral transporter slc43a2 (13.8-fold; P = 0.025). These changes suggest enhanced digestion and amino acid absorption, although functional confirmation is required. In contrast, EGTT was downregulated in pyloric caeca by both BSG (0.32-fold, P = 0.005) and BSGPO (0.38-fold, P = 0.010), whereas slc43a2 only responded to BSGPO (0.12-fold, P = 0.014). slc7a3 differed between BSG and BSGPO (P = 0.006), but neither differed from control. Notably, the mid-intestine showed no significant gene response. BSG diets modulated intestinal SLC transporter expression in a region-dependent manner, with broader responses in the BSGPO group. The distal intestine showed the strongest modulation, involving eight responsive genes associated with peptide digestion and amino acid transport. In contrast, the lack of response in the mid-intestine suggests localized intestinal effects. alp expression was unaffected, suggesting preserved mucosal homeostasis.