The alternative conceptions that students hold put a brake on subsequent meaningful learning, and therefore, the identification of these wrong ideas is crucial for effective teaching and academic success. Undergraduate STEM students often perceive Chemical Thermodynamics as a difficult subject, in which entropy has been pointed out as a threshold concept. In this paper, the prevalence of two alternative conceptions about entropy of first-year undergraduate students is studied by analyzing quantitative and qualitative results before and after instruction. It was found that students hold alternative conceptions about the conservation of entropy, whose prevalence depends on the specific context of the question, and that they strongly relate entropy to visual disorder. To some extent, the approach of using instructional videos and qualitative questionnaires as a teaching method was successful in enhancing students' understanding. The results of this research can be valuable for developing effective evidence-based curricula to improve teaching and help students deeply understand fundamental thermodynamic concepts.