This study examines the effect of internal audit unit independence and staff adequacy on the effectiveness of internal control system of tertiary educational institutions in Adamawa state Nigeria. This study employs survey research design. Data were collected using the questionnaires from the eight (8) TEIs were by 140 respondents were analyzed as a sample using Descriptive statistics and Chi-square technique. The main findings of this study are that internal audit unit of tertiary educational institutions in Adamawa State are not effective because they lack independence and are short of adequate staff, more so, they are not timely in their internal audit reporting. This phenomenon has contributed to the ineffectiveness of internal control system of the institutions. The study recommends that internal audit unit should be established as a separate department/unit to serve as custodian of internal control system, sufficient and competent staff should be recruited for the unit.