This study was carried out to identify organisms associated with banana deterioration and effects of storage on nutritional compositions of bananas. There is high cultivation and consumption of bananas in Nigeria. However, high post-harvest loss due to microbial rot remains an albatross. Aspergillus niger and Alcaligenes faecalis were isolated from rotten M. sapientus fruit while Rhizoctonia solani and Proteus vulgaris were isolated from M. acuminata fruit. However, Streptococcus pyrogens were isolated from both M. sapientus and M. acuminata. The percentage proximate content of the macronutrients, moisture, carbohydrate, ash, crude protein, crude fiber, and lipid was carried out on banana fruits stored for 5 days. The mean proximate composition of M. sapientum on the fifth day of storage showed a decrease in carbohydrate (from 18.807 to 5.334%) and lipid (from 3.292 to 2.874%) content, while an increase was observed in the moisture content (from 75.493 to 81.987%), protein (1.713 to 1.947%) and ash contents (1.937 to 1.969%). The results obtained showed that fruits stored at 4oC+1 in a refrigerator for 20 days stayed for a longer time before initiation of ripening, compared with fruits stored in moistened sawdust for 7 days and fruits stored in polyethylene bag moistened with KMnO4 solution for 3 days. The results obtained from this work showed that refrigeration was the most effective storage condition for prolonging the shelf life of bananas.