The COVID-19 pandemic forced Higher Education institutions all around the world to revise their praxis and update tools and numerous procedures. This study offers a comparative analysis of three Latin American students’ and instructors’ perspectives on a selection of both the pedagogical and emotional aspects of higher educational life that were affected. The report is about the participants’ perception of others’ empathy, their evaluation of the organization of teaching and learning and of collaborative learning experiences, their appreciation of the quality of learning assessment practices, and, eventually, their perception of learning. An exploratory study was carried out, based on survey research in Likert-scale form, responded to by 2742 students and 926 instructors. Significant differences were found among subsamples, with Chilean students and instructors having less favorable views in all dimensions compared with their Mexican and Ecuadorian counterparts; also, differences were found with respect to educational levels, discipline areas, and participants’ gender. This study contributes with a double-sided view of both protagonists’ perspectives (students’ and instructors’) to reinforce the importance of instructional design, instructor-student bond, meaningful and realistic assessments that allow for the application of knowledge, and opportunities for feedback in post-pandemic virtual education.