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At the onset of the COVID-19 pandemic, higher education institutions (HEIs), have been mandated to protect employees from the threats of COVID-19. During the implemented lockdown in the Philippines, only essential school workers (ESWs) were permitted on site, limiting contact and mobility. As such, this study sought to describe the perceptions of ESWs of a selected higher education institution in Metro Manila, Philippines, and how the HEI capacitates them in compliance with national guidelines. Focus group discussions (FGDs) were conducted among four (4) sectors of ESWs: security, maintenance, health services, and office staff. The FGDs were conducted during the period of Enhanced Community Quarantine period year 2021. A total of twenty-three (23) ESWs participated in this qualitative study. Thematic analysis was used to draw insights from the narratives of the FGDs. Results show three (3) emergent themes from the FGDs namely: (l) Physical and Mental Health implications, (2) Changes in Personal Life, and (3) Identified Risks during Working Hours. This study highlights that from the perspective of ESWs, the identified higher education institution strives to comply with the Philippines' Inter-Agency Task Force for the Management of Emerging Infectious Diseases (IATF) guidelines through various expressions of capacitation to protect them from the threat ofCOVID-19. However, results also demonstrate challenges that deter full compliance and consistent implementation of the guidelines across the said institution.