The aim of the study was to assess the effect of internal controls on profitability of supermarkets in Kenya. The specific objectives used were; to assess the effect of book keeping on profitability of supermarkets in Kisii town, to assess the effect of approving of transactions and to evaluate the influence of procurement procedures on profitability of supermarkets. From the study, it was clear that supermarkets undertake emphasis on creating the knowledge of the internal control procedures for supermarkets to be complying with the systems of control. The study established that financing of cash to procurement depend of efficiency and accurate data confine book keeping in payment. Numerous procurement procedures have helped in assess and improving the effectiveness of profitability. The supermarkets firms have formalized policies of control for all activities which allows for good and efficient control of stock out. This study concluded, that accepted the relationship between book keeping procedures on profitability by receiving of cash, accounts payment of goods, sales of stock and unlimited access to stores. The correlation and regression analysis were engaged in the study. Standard variation measured on the observed values from their mean.