Introduction: The Bocachico Prochilodus magdalenae, an endemic herbivorous/detritivorous fish from the Magdalena River basin, is the region’s most important fishing resource, with high ecological and socioeconomic significance. Its populations have declined significantly due to fishing pressure and anthropogenic environmental stressors, including wastewater discharge, infrastructure projects, and material extraction. Understanding the characteristics of its digestive tract is a crucial knowledge gap, hindering the comprehension of nutritional and physiological processes vital for aquaculture and both in situ and ex situ conservation efforts. Objective: To characterize the morphological, histological, and histochemical features of P. magdalenae’s gastrointestinal tract (GIT) and relate them to its feeding habits. Methods: Fifteen adult specimens from the Sogamoso River (Santander, Colombia) were analyzed using standard morphological measurements and histological and histochemical staining techniques for tissue structure and mucin distribution analysis. Descriptive statistics were used for morphological analysis. Results: Specimens averaged 24.66 cm standard length, 291.77 g weight, and 1.02 condition factor, with a mean GIT weight of 12.02 g. The digestive tract showed four distinct regions: oropharyngeal cavity, esophagus (mean length 1.26 cm), stomach, and intestine (mean length 88.18 cm). The esophagus contained abundant acinar glands, producing neutral and acidic mucins, with acidic mucins predominating. The U-shaped stomach showed simple columnar epithelium with tubular gastric glands producing only neutral mucins. The intestine, lined with simple columnar epithelium, exhibited differential mucin distribution: high neutral mucins anteriorly and predominantly acidic mucins in middle and posterior segments. Conclusions: The gastrointestinal characteristics align with its feeding habits, particularly the elongated intestine and thick pyloric muscular layer. The distinct mucin distribution pattern, especially the carboxylated acidic mucins in the middle and posterior intestinal segments, supports nutrient absorption functions. These findings provide crucial reference points for fish welfare assessment, pathogen response in aquaculture, and environmental impact evaluation in natural habitats.