Kenyan SACCO segment makes up a considerable percentage of the country’s savings and this has spurred economy and social development. It has been established that internal environment has a great bearing on the performance of SACCOs. This study investigated the relationship between internal control systems and performance in SACCOs in Nyeri Central Sub-County and was guided Restitution and Internal Control Theory, Agency theory and Control theory. Internal controls were looked at from the perspective of Control Environment, control activities, Risk Assessment and Monitoring all focused on the performance which measured profitability and investment returns. The target population was 26 operating SACCOs in Nyeri Central Sub-County and the respondents was 78 employees working in this SACCOs who were categorized into the loan managers, internal auditors and financial analysts. The research was conducted using both quantitative and qualitative approaches; adopting cross-sectional survey research design. The relevant data was collected using questionnaires, out of 78 employees 68 responded representing 87.2% response rate. Collected data was analyzed using statistical package for social sciences (SPSS) to generate descriptive statistics. Effects of internal controls on the financial performance of SACCOs in Nyeri central sub-county were measured using multiple regression analysis. The results indicated that internal control environment, risk assessment control and activity control had a positive and statistically significant effect on financial performance of SACCOs. Monitoring had a positive but statistically insignificant effect on financial performance of SACCOs. SACCOs should come up with policy that ensures regular and systematic review of the internal control systems and ensure that issues raised are addressed appropriately.