The attainment or otherwise of the primary objective of business, which is profitability is dependent on the effectiveness of controls inherent in its processes. The most susceptible to the misuse of resources due to lack of controls are the small scale enterprises (SSE). This leads to the death of seven out of every ten SSE established in their first two years. This study examined the effect of management controls of SSEs on their profitability. The use ordinary least square regression was employed in testing the research hypothesis formulated. Survey data was collected through the use of questionnaires. The study observed that internal control system has a positive significant effect on the financial performance of SSEs. The study therefore concludes that the establishment of controls such as preventive, corrective and detective controls forestalls organizations profit from leaks.