Objective To evaluate the effect of methanolic extract of Syzygium cumini (L.) Skeels (S. cumini) seeds on the major organs in an animal model of diabetes through biochemical and histopathological studies. Methods The methanolic extracts of S. cumini seeds (100 and 200 mg/kg body weight) were administered to alloxan-induced diabetic rats daily, with fasting blood glucose levels being measured by glucometry at one-day interval for a duration of two weeks. Biochemical assays to evaluate changes in the functions of the heart, liver, pancreas and kidney were carried out. Histopathological changes in the diabetic rat organs (pancreas, liver, heart, kidney and spleen) were also observed after the 14 days of treatment with the extracts. Results Oral administration of methanolic extracts of S. cumini seeds (100 and 200 mg/kg body weight), with gliclazide as a positive control (25 mg/kg), showed beneficial effects including lowering blood glucose levels (P < 0.001), improved heart and liver functions, and hyperlipidemia due to diabetes. At 200 mg/kg, the extracts reversed cardiac and liver damage caused by alloxan. Conclusions In addition to the anti-hyperglycemic activity of methanolic extracts of S. cumini seeds, the extracts demonstrates potential to minimize cardiac and hepatic complications.