Agriculture and its allied sectors serve as the world’s largest employer, ensuring food security and income generation of the majority of population in developing countries. Thus, the contribution of agricultural research institutes is crucial in achieving the Sustainable Development Goals set by 2030, spotlighting SDG 2-Zero Hunger. In such agricultural research institutes, Key Performance Indicators (KPIs) are imperative in assessing a range of key performance drivers intended to realise an organisation’s vision, which is based on SMART objectives. The purpose of this study was to evaluate the existing KPI implementation status at Sri Lankan research institutions with an agricultural focus and to uncover any limitations that might prevent the effective execution of a performance management system (PMS). The research institutes’ top administrative officers were approached via semi-structured personal interviews that included 15 inquiries capturing key aspects of KPIs, such as formulating, establishing, and measuring, conducted through an Online Video Conferencing Facility. This was followed by qualitative research methods to analyse the data. Interviewees’ responses, expressed as attitudinal statements, were transcribed and analysed using the MAXQDA 2022 qualitative data analysis software. The results were derived after following the steps of thematic analysis by identifying several key themes, particularly: Technology Integrated Performance Management Systems, Research for Society, Institutional Research Management, Research Collaboration, and Research Commercialisation. Based on the relationships revealed via the strategic adaptation of performance management practices, research institutes could strengthen the financial and administrative stability. Indeed, a well-balanced research environment would be facilitated by an effective performance management system guided by KPIs to generate outputs that are well acknowledged by society in order to ensure food security and meet SDG 2 Zero Hunger by 2030.