In order to improve the quality of education in Indonesia, the government provides assistance in the form of grants to college programs. Unfortunately, the many irregularities occurring in the management of grants. Cases of fraud occur in college as an educational environment that is expected to be an example other institutions in terms of accountability in the management of funds. Internal audit can effectively minimize the possibility of misuse of these funds. 
This study aimed to compare the Monevin implementation (of monitoring and internal evaluation) which functions as an internal audit program grant at the Islamic University of Indonesia Yogyakarta and Atma Jaya Catholic University, Jakarta. Research using qualitative methods of analysis pairing patterns and the data obtained from the document, archive footage, interviews and participant observation. The results showed that the amount of compensation, employee competence and work culture influence the effectiveness of the internal monitoring and evaluation of the grant program.