Public commuter transport sector is a key social facility that not only provides mobility, but also generate jobs and enable economic growth. In Kenya, the sector adopts a privately owned para-transit mode, that operates along largely defined routes,and are managed by SACCOs. This study focused on the effect of general information controls and application controls on the financial performance of the public commuter transport sector SACCOs. The study adopted a mixed method approach in data collection that included collection of primary data through the use of questionnaires, while secondary data was obtained from audited financial statements of the public commuter transport sector SACCOs. Key informant interviews were also conducted. The study was anchored on the agency theory to assess the effect of the information flow on financial performance, and to establish if strong IT controls mechanism enhanced performance. The study discovered a unique peculiarity in that independent variables account only 7.6% of the financial performance of the public transport sector SACCOs, implying that strong IT controls did not account for financial performance in the public commuter transport sector SACCOs. The study recommend the implementation of a risk-based approach to Information Controls, in which the SACCOs identify and prioritize high-risk areas that require stringent controls while allowing more flexibility in lower-risk areas to mitigate the risk of poor financial performance.