COVID-19 has presented a novel pedagogical challenge in dealing with the sudden shift from classic instruction to emergency remote teaching (ERT). It had an impact on the well-being and mental health of lecturers, increasing burnout risk. A cross-sectional, quantitative, qualitative and analytical online study was conducted to collect participants’ sociodemographic data, responses to ERT open-ended questions and mental health assessments using relevant instruments (CBI for burnout, Resilience Scale, DASS for depression, anxiety and stress, SWLS for satisfaction with life). High personal burnout levels were found in 41.2% of participants, high work-related burnout in 37.3% and high student-related burnout in 15.7%. Satisfaction with life, sleep routine changes and stress were determinants for personal burnout; stress and resilience for work-related burnout; satisfaction of life and sleep routine changes for students-related burnout. Opportunities for pedagogical innovation were pointed out as the main advantages to ERT, while the main negative impacts were on practical lessons and social interaction. Students and lecturers’ safety and adequate institutional support might be insured, considering their expectations and needs, promoting mental health. Combining the advantages of online and traditional methods in a so-called “blended learning” approach, with close collaboration and communication between all those involved, appears to achieve better results.