This study explores the significance of practical experimentation in the teaching of life and earth sciences (LES), particularly in the context of studying microorganisms. The research focuses on identifying key challenges that hinder the effective use of experiments in science classrooms and highlights the potential role of simulation as a remedial tool. A mixed-method approach was employed, including interviews with teachers and surveys targeting both teachers and students. Two main issues were identified: inadequate infrastructure for practical work in two educational institutions (a middle school and a high school) and varied student perceptions regarding experimental activities. The findings revealed that, under current conditions, the laboratories at these institutions fail to support active learning and scientific knowledge development. Most scientific activities are conducted in a theoretical context due to poor laboratory facilities and management. Additionally, students expressed a lack of motivation, partly due to their awareness of the poor laboratory conditions and the unengaging teaching methods employed. This research underscores the potential of simulations as a valuable tool to address these challenges and improve the LES teaching-learning process, without replacing traditional experiments. The study emphasizes the need for improving both the infrastructure and the pedagogical approaches to enhance the educational experience in the sciences.