Due to the COVID-19 pandemic, Higher Education Institutions (HEI) replaced regular face-to-face teaching with online teaching and learning. However, the shift caused several academic and social concerns for students, such as lack of academic support, lack of adequate resources to support online teaching, lack of socialization, stress, anxiety, and lack of motivation in attending classes. This research evaluates the impact of HEIs support, faculty support, and resources available on the academic and social concerns of students in HEIs during the pandemic. 11,114 students across the HEIs in Sultanate of Oman participated in an online national survey. Regression and factor analysis were used to verify the research model developed based on the literature review. Results showed that HEI support and faculty support significantly affect university students' academic and social concerns. Furthermore, resource availability was found to affect the academic concerns of students but not their social concerns. This research recommends strategies for HEIs and faculty to promote faculty-student interaction using both synchronous and asynchronous modes to reduce student concerns and motivate them to engage in online classes.