Most universities stopped face-to-face instruction in March 2020 due to the COVID-19 pandemic and completed the spring 2020 semester through online instruction and assessment. At our institution, the online instructions continued until the summer of 2021. In fall 2021, the university decided to delay the full return of faculty, students, and staff to campus for the first three weeks. The first three weeks of instruction of our courses was conducted on-line and then was changed to face-to-face for the remainder of semester. Significant variation in student performance was observed between similar courses offered prior to, during, and after the online instruction due to COVID-19. The passing rates for similar courses offered during this period have been compared in this paper. A gradual decline in the knowledge of prerequisite topics following the first online semester is noticed, which indicates that many students were assessed in such a way that they passed important prerequisites courses with minimum knowledge. The decline is based on several factors that include challenges that students and instructors have faced during the online instructions, as well as the way students' knowledge was assessed, especially with online exams where there has been a notable increase in scholastic dishonesty. The factors that resulted in lower student academic performances are identified.