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This study investigates the impact of active learning on the acquisition of competencies and learning outcomes in the context of organic chemistry education. Specifically, this study focuses on the implementation of active learning in the extraction of an unknown mixture of organic compounds using acidic and basic solutions. This research is based on an “ex post facto” study involving 40 first-year undergraduate students who are pre-service chemistry teachers at a Slovak public university. This study aims to analyse students’ performance, identify common problems encountered, and assess the advantages and disadvantages of the active learning approach. The data collection instruments included a structured report on best practices in university education and a questionnaire to evaluate the experiences and assessment systems used. This study compares the effectiveness of online and face-to-face teaching methods for practical chemistry coursework. The key findings from the comparison of these methods are the differences in learning outcomes achieved, e.g., answers to tasks 2–6 from the questionnaire. Group B respondents had a higher number of correct responses and lower variability compared to Group A respondents. This difference may indicate an improvement in comprehension and effectiveness of instruction over the period. Differences in scores between the groups may be due to random variability in the composition of the groups, which we found through statistical analysis. Full-time students felt more engaged and more satisfied. More than half of the students said that they preferred face-to-face interactions to help them better understand the material. While online instruction provided greater flexibility and accessibility, students felt that they lacked hands-on interaction, which negatively impacted their acquisition of practical skills. The results indicate that active learning, particularly hands-on laboratory exercises, had a positive impact on the acquisition of professional competencies and students’ learning outcomes. This study also highlights the advantages of active learning in practical chemistry education.