Objectives: This study aimed to analyze how pedagogical practices and affective states during emergency remote teaching influence professors’ perspectives on their capabilities and the professor-student relationship. Method: We used a nonexperimental quantitative design, collecting data through an online survey during the first year of the pandemic. Participants were recruited using a non-probability sampling method. A total of 636 university professors from Chilean universities participated. We performed descriptive and correlation analyses between variables. Also, to gain a deeper understanding of the factors influencing perceptions of the professors’ competence and the professor–student relationship, we conducted linear regression models. Results: A higher perception of pedagogical competence was related to male professors reporting a high evaluation of teaching quality and a high diversification of assessment strategies. A better professor–student relationship was related to female professors reporting a high level of tutoring activities and activities in which students work collaboratively. Additionally, unpleasant affective states were experienced at a higher rate by younger and female professors. Conclusions: Variables that make up the perception of professor competence and the professor–student relationship were identified, relating to gender and pedagogical practices, such as diversification of assessment strategies, tutoring, and collaborative activities. Implications: The results can guide future institutional actions to improve conditions and establish guidelines for quality virtual education in the post-pandemic scenario.