The COVID-19 pandemic severely disrupted European universities’ educational process. With the vaccination rollout, in-class instruction broadly resumed beginning in September 2021. In order to mitigate the risks of SARS-CoV-2 transmission, European universities apply COVID-19 containment protocols. The aim of this paper is to evaluate the COVID-19 containment protocol that Greek universities implemented in order to fully reopen in the fall of 2021 and for the entire academic year 2021–2022. A case study was conducted at the Department of Industrial Management and Technology, University of Piraeus (Athens’ port), Greece. Data were collected from November 2021 to July 2022 and a quantitative statistical analysis (descriptive and inferential) was performed. A total of 330 unique (and 43 reinfections) COVID-19 cases were confirmed, including 241 undergraduate students, 73 postgraduate, and 2 doctoral students, 10 faculty, and 4 administrative personnel. Contact tracing reported four confirmed and eight potential cases of in-classroom transmission. The person in charge of implementing the COVID-19 containment protocol in the department ordered more than 6000 rapid tests during this period. The Department of Industrial Management and Technology at the University of Piraeus used a rigorously monitored and coordinated strategy of vaccine promotion, screening/testing, contact tracing, isolation, and quarantine in order to control COVID-19 transmission. The results show, on one hand, that the protocol’s implementation is effective and leads to in-classroom transmission minimization and, on the other hand, verify the hypothesis that the department’s confirmed COVID-19 cases are less (with a mean percentage difference of 50%) than the community’s respective 18–39 age group.