Due to COVID-19, universities have been facing challenges in generating the best possible experience for students with online academic training programs. To analyze professors’ expectations about online education and relate them to student academic performance during the COVID-19 pandemic, and considering the socio-demographic, entry, and prior university performance variables of students. A prospective longitudinal design was used to analyze the expectations of 546 professors (54.8% male) in T1. In T2, the impact of the expectations of 382 of these professors (57.6% men) was analyzed, who taught courses during the first semester to a total of 14,838 university students (44.6% men). Professors’ expectations and their previous experience of online courses were obtained during T1, and the students’ academic information was obtained in T2. A questionnaire examining the Expectations toward Virtual Education in Higher Education for Professors was used. 84.9% of the professors were considered to have moderate to high skills for online courses. Differences in expectations were found according to the professors’ training level. The professors’ self-efficacy for online education, institutional engagement, and academic planning had the highest scores. The expectations of professors did not directly change the academic performance of students; however, a moderating effect of professor’s expectations was identified in the previous student academic performance relationship on their current academic performance.