Several studies have highlighted the impact of technostress and physical discomfort on employees' productivity. With the advent of virtual and flexible learning in the Philippines due to the Covid-19 pandemic, teaching and non-teaching employees became susceptible to physical discomfort and technostress. The study uses partial least square structural equation modeling (PLS-SEM) to examine the interplay of technostress and physical discomfort to employees' productivity at MSEUF campuses. The study’s participants were the employees of MSEUF, including department heads, faculty, and non-teaching employees. The study employed quantitative research with a causal research design to measure the relationship between technostress and physical discomfort and productivity. Using the WarpPLS 8.0, the study measured the sampling adequacy using the Inverse-square root method and Gamma-exponential. Also, the measurement model and structural model were evaluated using reliability and validity test like convergent and discriminant validity. The result shows that technostress positively affects physical discomfort with a moderate coefficient of determination (R²) level. While technostress and physical discomfort significantly and negatively affect employees' productivity, with a moderate level of R². Furthermore, the result implies that during this shift in the educational systems in the Philippines, employees must be given enough support and assistance to perform at their full potential to deliver and be productive, despite the different challenges.