(1) Generating the need to impose social distancing to reduce the spread of the virus, the COVID-19 pandemic altered the ways in which the teaching process normally happens. The aim of our study was to determine the impact of online teaching on medical students during this period. (2) Our study included 2059 medical, dental and pharmacy students from the University of Medicine and Pharmacy "Grigore T. Popa", Iasi, Romania. We used a modified metacognition questionnaire after translation into Romanian and validation. Our questionnaire included 38 items, and it was divided into four parts. Academic results and preferences regarding the on-site or online courses, information regarding practical training, self-awareness in terms of one's feelings such as anger, boredom and anxiety and also substance use linked to online teaching, and contextualization of the relationship with colleagues, teachers, friends and family were among the most important points evaluated. A comparison was made between preclinical and clinical students. A five-item Linkert-like scale was used for rating the answers in the last three parts that evaluated the impact of the SARS-CoV-2 pandemic on the educational process. (3) Preclinical medical students, compared to preclinical dental students, obtained statistically significant improvements in their evaluation results, with fewer failed exams (p < 0.001) and with similar results being obtained by comparing dental with pharmacy students. All students obtained statistically significant improvements in their academic results during the online evaluation. A statistically significant increase in anxiety and depression with a p-value of <0.001 was registered among our students. (4) The majority found it difficult to cope with this intense period. Both teachers and students found it difficult to adjust on such short notice to the challenges posed by the new concept of online teaching and learning.