The COVID-19 pandemic has caused the loss of several human lives and the global transformation of education systems throughout the world. It resulted to the fast transition of face-to-face teaching to distance education, especially in the developed countries, to prevent the dissemination of the pandemic among the students. However, because of the requirements and challenges of the online classes, the face-to-face courses had been restored with several restrictions. The objective of this research is to explore the perceptions of secondary school science teachers regarding the classroom management after the period of the confinement. The qualitative data have been received through individual and focus group interviews with six professors certified (mathematics, physics, chemistry and technology and life and earth sciences) and three of their pedagogical counselors. Regarding the barrier measures and other imposed restrictions, the results have pointed up the difficulties of the classroom management relating to the factors such as: classroom climate, communication, cooperation, physical organization of the class, conduct of practical work, management of behaviors and discipline and reduction of the feeling personal and professional efficacy. Concerning the convenient pedagogical practices that can help them to teach better, participants requested the implementation of professional development programs, related to the differentiated pedagogy and offered suggestions toward secondary school decision makers.