Traditional face-to-face classes were replaced with online learning when the COVID-19 pandemic happened. Students were unfamiliar with the virtual setup, as well as the technological challenges, which led to dissatisfaction and affected their academic performance. This research study surveyed 230 engineering students and applied conjoint analysis to analyze their preferences in online learning delivery. Using SPSS Statistics software, we revealed the top three attributes for delivery type: interaction, flexibility, and proctored exam. In addition, the most favored combination from the generated stimuli was a form of blended mode delivery. The synchronous meetings and asynchronous activities allowed students to manage their time efficiently. It could be deduced from the findings that students highly preferred the combination considering learner–instructor, live chats, real-time lecture meetings, and automatic availability, with a focus on synchronous online learning modes. Higher education institutions may reflect on the results of this study to reassess the online learning environment they implement among students. Incorporating a student’s learning style to determine the relationship between their preference for online learning delivery type will be helpful for further research through application and study extension. It is suggested that the perceptions of instructors and students enrolled under different learning modalities and their effectiveness should also be addressed. This is a recommendation for future research to consider. Especially near the end of the COVID-19 pandemic, traditional face-to-face learning was being implemented. Thus, future studies may want to consider an analysis of the behavioral intentions of students. On the other hand, analyses such as student behavioral intentions for the future applications of the different modalities and comparisons thereof may be conducted to enhance the implications for, policies of, and strategies of universities.