The paper presents on and motivates the significance of choosing an appropriate postgraduate Applied Information Systems (AIS) research methodology and application in higher education institutions. Research education has become a matter of concern as there are low completion rates of masters student dissertations. This study addresses the issue of inappropriate and misalignment of IS research methodologies of AIS masters' and MBA dissertations at the North-West University (NWU) to determine whether the research approach used by both disciplines was relevant to their studies. The choice of selecting an appropriate research methodology is a tedious task with which many researchers are confronted during the research process. The principal research objective was to explore AIS and MBA students' ideological ways of comprehending information and dissertation requirements, by preparing them to undertake sound research projects that culminate in a masters' dissertation and improve research completion rates. The alleged problem is that AIS masters' and MBA students use a particular research methodology for rather negative reasons and consider it to be the most appropriate for IS research. A quantitative research approach was adopted and a structured framework was used as an instrument for data gathering which targeted 103 from AIS masters and MBA 97, all together to taled 200 dissertations. The findings based on the data indicate that there is a lack of a conceptual matrix, supervision guidance, furthermore, it evidenced that there is badly-structured research dissertations of MBA. There is a need for graduate school to be introduced to the use of an appropriate conceptual matrix into MBA research approaches.