The COVID-19 pandemic compelled the global and abrupt conversion of conventional face-to-face instruction to the online format in many educational institutions. Urgent and careful planning is needed to mitigate negative effects of pandemic on engineering education that has been traditionally content-centered, hands-on and design-oriented. To enhance engineering online education during the pandemic, we conducted an observational study at California State University, Long Beach (one of the largest and most diverse four-year university in the U.S.). A total of 110 faculty members and 627 students from six engineering departments participated in surveys and answered quantitative and qualitative questions to highlight the challenges they experienced during the online instruction in Spring 2020. Our results identified various issues that negatively influenced the online engineering education including logistical/technical problems, learning/teaching challenges, privacy and security concerns and lack of sufficient hands-on training. For example, more than half of the students indicated lack of engagement in class, difficulty in maintaining their focus and Zoom fatigue after attending multiple online sessions. A correlation analysis showed that while semi-online asynchronous exams were associated with an increase in the perceived cheating by the instructors, a fully online or open-book/open-note exams had an association with a decrease in instructor’s perception of cheating. To address various identified challenges, we recommended strategies for educational stakeholders (students, faculty and administration) to fill the tools and technology gap and improve online engineering education. These recommendations are practical approaches for many similar institutions around the world and would help improve the learning outcomes of online educations in various engineering subfields. As the pandemic continues, sharing the results of this study with other educators can help with more effective planning and choice of best practices to enhance the efficacy of online engineering education during COVID-19 and post-pandemic.