Due to the outbreak of the COVID-19 pandemic, many colleges and universities converted to remote delivery after March 2020. The Spring 2020 semester was split into two sections: half-semester face-to-face learning and half-semester online delivery. It provides a unique opportunity to study the effectiveness of blended learning. We examined students’ perceptions of blended learning from 4 STEM courses taught by two instructors in Spring 2020 (two courses in Agricultural Science and two courses in Geoscience). Although students’ ratings of their blended learning experience in Spring 2020 were mixed, the vast majority of students in the survey chose blended learning as the preferred approach over online or face-to-face delivery only. Pure online delivery was the least favored option for students in this study, but online homework assignments, quizzes, and videos were perceived as useful tools to improve the online component of the blended course. This investigation was carried out to understand the best practices of using web-based tools in the blended delivery format to enhance the effectiveness of student learning activities and help instructors improve the teaching strategy as the pandemic continues. Interweaving online tools with traditional face-to-face instructions would enrich students’ learning environment by providing interactive and community-building experiences.