The aim of this study was to investigate the prebiotic potential of pectin hydrolysates that were extracted from agroindustrial waste (apple pomace—AP and passion fruit peel—PFP) and were added to the diet of silver catfish (Rhamdia quelen). A 49‐day biological assay was conducted, and five test diets were evaluated: one diet was a control diet and the other four diets included pectin hydrolysates (2.5 and 5 g/kg). At 49 experimental days, biometric data and biological material were collected to determine the performance, plasma and liver and histological parameters and to evaluate the intestinal contents. The results were analysed by the normality test, which was followed by an analysis of the variance; the treatment means were compared by an orthogonal contrast analysis at a 5% level of significance. The inclusion of 2.5 g/kg apple pomace hydrolysates resulted in a greater production of butyric acid, increased thickness of the muscular layer and higher goblet cell count in the intestine. The inclusion of 5 g/kg apple pomace hydrolysates led to a greater concentration of liver protein. Further studies are needed to increase the knowledge about the use of these additives in the diet of silver catfish and to establish levels that allow greater gains for the species.