Arapaima spp., the world's largest scaled freshwater fish, native to the Amazon and Essequibo river basins, are valued in aquaculture for their rapid growth and ornamental appeal. However, reliance on natural breeding and parental care in earthen ponds results in variable fingerling survival, hindering production. This study investigated the morphology and functionality of the digestive system of Arapaima sp. fingerlings from the Peruvian Amazon and evaluated the feasibility of early weaning onto compound diets to optimise growth and survival. Fingerlings were collected from a pond at 3.19 ± 0.03 cm total length (TL) and reared in a recirculating aquaculture system at 29 ºC under a 12L:12D photoperiod. Fish were successfully weaned from Artemia spp. nauplii onto an experimental compound diet (60% protein, 15% lipid) from 3.26 ± 0.02 cm TL within three days. Histological and gene expression analyses of key digestive enzyme precursors and appetite-regulating peptides (α-amylase, phospholipase A2, lipoprotein lipase, trypsinogen, chymotrypsinogen, pepsinogen, and peptide YY) revealed a mature digestive system, with enhanced digestive efficiency observed at 5.05 ± 0.34 cm TL. Based on digestive enzyme expression profiles and gut morphology, early juvenile Arapaima sp. possess a digestive physiology consistent with that of an omnivorous species with a preference for animal prey. The middle intestine was identified as a key site for fatty acid absorption and feed intake regulation. This study presents a novel, comprehensive analysis of digestive enzyme gene expression and associated tissue morphology in the genus Arapaima. It provides new insights into their digestive physiology and establishes the feasibility of early weaning