The study explored the influence of research mentoring on research publications output during COVID-19 in a selected Higher Education Institution (HEI) of the Eastern Cape Province as the incessant poor publications from the dissertations and theses of postgraduates upon completion of their studies prompted the researchers to want to understand the nature of the mentorship experiences during the COVID-19 pandemic. The study was situated within an interpretivist paradigm which aided in the interpretation of the facts and adopted a case study design within a qualitative research approach. The participants for the study comprised eight research supervisors, and eight master’s and doctoral students purposefully selected as information-rich participants. Semi-structured interviews were utilised to collect data. Data collected were analysed thematically. Findings of the study revealed that there was a dearth of research mentoring by research supervisors that adversely affected research publication output in the rural HEI, especially during the COVID-19 era. Additionally, supervisors struggled with online supervision, which strained the relationship between supervisors and their students. Furthermore, the study revealed that both supervisors and students lacked skills and knowledge of paper writing. The study recommends that there should be a call for student mentoring and development in research seminars, article writing seminars, and writing for publication workshops to develop and promote academic success in higher education institutions. It is anticipated that a strengthened system of mentoring and development, which is cognizant of COVID-19, will help novice writers comprehend articles published through the holistic guidance of their mentors rather than mentors leaving them to sink or swim. Keywords: COVID-19, Higher education institutions, Mentoring, Postgraduate students, Research output