The paper studies the various institution-specific factors that affect the research outcome using fuzzy-set qualitative comparative analysis (FsQCA). The study is done in state university-affiliated institutions in South Indian states—Andhra Pradesh, Karnataka, and Kerala – with a sample size of 215. The frequency of the presence and absence of core and peripheral factors from the FsQCA analysis helps to identify which factors, the presence or/and absence, help improve the research outcome. The number of students enrolled, the percentage of faculties with higher qualifications, the enrolment percentage in extension programmes, enlistment in value-added activities, and ICT-enabled facilities are the core factors that affect research outcomes in institutions. The methods and findings have implications for understanding the core and peripheral factors that impact a successful research outcome. This can help build a useful research implementation, assessment, and prediction model for institutions. Understanding these critical factors helps institutional leadership frame policies, allocate budgets, allocate resources, and make other major decisions that enhance and nurture research.