The onset of the COVID-19 virus has somewhat rattled the workforce in many aspects. COVID-19 is a worldwide health problem that started in the year 2019 but became a global concern in the succeeding years to the present date. Teachers and other working personnel continued their work in spite of the academic lockdown caused by the COVID-19 pandemic. This research therefore explored on the work engagement, job satisfaction and challenges met by the employees of the University of Baguio. It also determined significant differences between the teaching and non-teaching employees. Furthermore, it also looked into the relationship between work engagement and job satisfaction as well as the challenges they met. A descriptive-survey method using a researcher-made questionnaire was used to gather information through a Google form, and only employees working during the pandemic and were willing to answer the survey were included. A 4-pt Likert scale was used to answer work engagement and job satisfaction and a T-test to determine the significant difference between the two groups. Spearman correlation coefficient computed the relationship between work engagement and job satisfaction. A frequency count was used to determine the challenges encountered. Statistically, showed that employees were moderately engaged and moderately satisfied with their job during the pandemic. A significant difference in terms of work engagement was determined but no significant difference in terms of job satisfaction. Work engagement and job satisfaction showed a strong positive relationship. The biggest challenge encountered by the respondents were internet and virtual access. The result of the study clearly shows that the employees did well in their job during the pandemic in spite of some challenges they encountered. Future study to look into the factors affecting work engagement and job satisfaction