This study was aimed to identify bioactive compounds and determine the anti-amoebic and organ protective potentials of Vernonia amygdalina prebiotic fraction of leaf extract. These were achieved by GCMS and histological analysis of the liver and large intestine of adult wistar rats. The rats were grouped into seven (I-VII.) made up of five animals each. Group I was fed with feed and water. Group II were fed with glucose, Group III were fed with rice and treated with 100mg/ml of extract per kg body weight. Group IV were fed with rice and treated with 200mg/ml of extract per kg body weight. Group V were fed with rice and treated with 300mg/dl of extract per kg body weight. Group VI was fed with rice and treated with 400mg/ml of extract per kg body weight whereas group VII were fed with rice only. Histological examination of the large intestine and liver tissues of the wistar rats in various groups revealed normal structure of the organs in all the groups with highly improved cytoarchitecture of the liver and large intestinal tissues for the group treated with 300mg/mL/kg body weight. In vitro evaluation of the 300mg/mL prebiotic fraction of V. amygdalina leaf extract and metronidazole against Entamoeba histolytica showed significant (p<0.05) anti-amoebic effects when compared with negative control (none treated). GCMS analysis identified 19 bioactive compounds which included 3 unique compounds including; phytol, Heptanediamide, N,N'-di-benzoyloxy-, and α- β-Amyrin. This study revealed that prebiotic leaf extracts of V. amygdalina contains bioactive compounds that are non-toxic and possess cytoprotective potentials.