The research aimed at establishing the factors that influence the adoption of Inter-organizational information system (IOIS )adoption in the universities in Kenya. Data was collected using both questionnaires and semi-structured interviews.The research findings showed that there existed factors that motivated IOIS adoption and others that hindered IOIS adoption. The findings are useful to the policy makers as it can help them to support the factors that motivate IOIS adoption, and suppress the factors that hinder IOIS adoption in order to encourage IOIS adoption the universities in Kenya.