The study sought to establish the effect of internal controls on the financial performance of SACCOs in the transport sector. The Kenyan transport sector accounts for about 8.3% of the Kenyan GDP. The sector faces inadequate financial performance due to weakness in internal controls, indicated by inefficient management, investment losses and non-compliance in the sector. The study specifically looked at the effect of management controls, access controls, accounting controls and information technology controls on the financial performance of the transport sector SACCOs in Murang’a County. The county was selected for the study because it has nurtured well-organized transport sector SACCOs including MTN, NTK and KST; all serving customers from different parts of the country. The research was founded on agency, contingency and stewardship theories. A descriptive research design was used for the study. A census approach targeting all the 19 SACCOs registered under the Ministry of Cooperative Societies Development in Murang’a County. Questionnaires were used to obtain the primary data while the secondary data was obtained from the SACCOs’ audited financial statements for five years from 2017 to the year 2021. Both descriptive and inferential statistics were used to analyze the data. With a response rate of 84.2%, the data was cleaned and then analyzed using regression analysis and the hypotheses of the study were further tested. The R square coefficients of 0.060, 0.041, 0.025 and 0.065 obtained representing the management controls, access controls, accounting controls and IT controls respectively, all indicated that the four independent variables had an insignificant effect on the financial performance of the transport sector SACCOs. Subsequently, the R Square obtained from the multiple regression of 0.399 suggests that the independent variables account for only 39.9% of the transport SACCOs’ financial performance. The study concluded that internal controls had no significant effect on the financial performance of the transport sector SACCOs. The study recommends that the Ministry of Cooperative Societies should have a policy to ensure that the SACCOs establish the required management, access, accounting and IT controls to aid in improving the financial performance of the SACCOs. Further studies should be carried out to determine other possible factors affecting the financial performance of the transport sector SACCOs.