The Covid-19 pandemic halted the normal operations of schools and universities around the world. Various educational institutions, including the Philippines Commission on Higher Education (CHED), adapted to the limitations caused by the pandemic and recommended online education to reach students and learners remotely. This research investigated the challenges to online engineering education in higher educational institutions (HEIs) (n=4) in Eastern Visayas, Philippines. Challenges and problems experienced by faculty (n=25) and students (n=421) were gathered through an online survey on December 2020 using Google Forms. Â Findings indicate that 98% of the respondents were gadget ready for online education for the first semester of SY 2020-2021, and the primary type implemented is Online Education Only (OEO) (n=369). The majority of the respondents (94%) believed that the quality of education suffered from the sudden shift to online education and 64% believed it is not as effective as the traditional face-to-face classroom interaction. Â Post Covid-19, 60% of the faculty prefers Blended Education (BE); while the students (65%) prefer the traditional classroom face-to-face interaction. The challenges faced by the respondents during the Covid-19 analysed through qualitative content analysis can be categorised into Personal Challenges, Limited Social Interaction, Technology Difficulties, Assessment Issues, and Concerns on Learning Materials and Methods. Â Â