In this paper, we aim to identify online teaching and learning practices that would be beneficial for blended and traditional on-campus education within STEM (Science, Technology, Engineering, and Mathematics) courses. Our university, as well as the majority of higher education institutions worldwide, has had few to no experience in delivering full online courses before 2020. The teaching process was, however, severely affected and modified by the COVID-19 pandemic, forcing an abrupt and unprepared shift towards online education. In this work, we look at the pandemic as causing a very favorable side effect that forced the university to study, test, apply, and evaluate the benefits and drawbacks of online education and assessment methods. The study is a result of joint efforts from different departments at the University of Aveiro, Portugal, connected to STEM undergraduate and graduate programs and is based on a questionnaire targeted towards students. In total, 167 valid STEM students’ answers have been collected and analyzed, both quantitatively and qualitatively. As the result, the best teaching and learning practices are identified and the main difficulties and obstacles experienced by students are detected. Some of the problems are common to many higher education institutions, such as the lack of teacher preparation in delivering quality online synchronous and asynchronous classes, technical limitations (network bandwidth/weak equipment), ineffective communication during synchronous classes, gaps in student skills, and low activity of some students and even teachers. We believe that the presented results would allow for improving future on-campus, distance, and blended learning courses, particularly through avoiding less effective teaching and assessment methods and favoring those techniques that students consider more efficient. This ultimately would lead to a more rewarding teaching/learning experience.