Accessing the nexus between MIS compliance and the academic institution performance is to a great extent dependent, reflective in the symbiotic relationship between the universities, polytechnics colleges, and its products, stakeholders and the outside world. The non-compliance in this unique feature resulted in the practical gap in institution performance due to the shortcoming of undermining MIS volatility, by limiting the elasticity rich potential of MIS compliance in Nigeria tertiary institution. Negate the exploration and maximization of the full benefits of MIS management, somewhat cannibalizing the manual methods. This divergence has found to be systematically responsible for the dwindling institution performance, in the area of supervision, admission, and graduation of students at much longer duration than projected in Nigeria and Sub-Sahara. It is the anchor of this study to investigate the impact of MIS on institutions performance focusing on the academic point of view at the Nigerian universities, polytechnics, that have a business college using a structural model to explore this inherent practical gap. The study revealed that cost/expense impact, people impact and performance effectiveness were positively related to enterprise performance and efficiency, growth, and development. The researcher strongly recommends the adoption of MIS compliance policy in a tertiary institution instead of depending on the old manual record management approach practised by Nigerian institutions of higher learning. Hence, this will improve the trust, confidence, and performance of every active participant in real currentissue/activities, either as a consumer, investor, suppliers, mediators, or in the process of input, processing and output stage, etc.