The study aimed to identify the work challenges encountered by the employees due to the pandemic, their current depression, anxiety, stress, mental well-being, and perception of the institution’s capacity to manage the current crisis and mental healthcare needs. Online surveys were utilized as a method. The results revealed that the top on the list of the work challenges encountered by most of the employees due to the pandemic was: internet connection, too many distractions at home, balancing work and personal life, general anxiety of getting infected, and technology-based communication like virtual meetings, while for teaching personnel doing modules, checking and monitoring students and conducting online classes were among their concerns. Out of 73 sample population, 64% were at normal level, 36% were at mild to extreme levels in depression subscale. About 58% were at the normal level for the anxiety subscale while 42% fell on the mild to extreme levels. For the stress subscale, 23% were mild to severe, and the rest were on a normal level. As to the wellbeing level, 22% of the samples were in the low level, 67% were in the average, and 11% were in the high level. Though most of the employees were confident towards the institution’s leaders in handling the crisis, they still felt worried about the impact of the pandemic on the institution. The employees strongly agreed on the necessity of the presence of mental health professionals in the institution and suggested conducting debriefing/processing to ease the mental and psychological burden brought by this pandemic.