Semi-autonomous government agencies within the state department of energy are critical to the taxpayer and the government for efficiency in public service delivery. Diverse studies have examined the role of internal audit on the organizational performance but do not link internal audit to organizational performance within semiautonomous state agencies in Energy department. This study thus sought to establish the influence of independence of internal audit on organizational performance of semi-autonomous agencies in the state department of energy in Nakuru County, Kenya. The study used correlational research design with the target population comprising 72 internal auditors and senior management of the five semi-autonomous agencies in the state department of energy in Nakuru County. It employed census method to study all the population of the study, implying that the sample for the study was 72 respondents. A Questionnaire was used to collect data. To ensure content validity, the researcher constructed the instrument in line with the research objective. A Cronbach alpha coefficient of 0.7 was computed implying that the instruments were reliable. Descriptive statistics including frequencies, mean and standard deviation were used in data analysis. Also, inferential statistics; Pearson correlation and linear regression were used. The study established that there is a statistically significant influence of internal controls on organizational performance of semi-autonomous agencies in the state department of energy in Nakuru County, Kenya. The study thus recommended that in order to improve on the organizational performance of these semi-autonomous agencies in the state department of energy in Nakuru County, the management should enhance their focus on the independence of the internal audits