Organic qualitative analysis is one of the challenging chemical concepts in students learning of chemistry. The West African Examinations Council chemistry chief examiners for years, have lamented on students’ poor performance in organic qualitative analysis at the senior high school level. This study, therefore, investigated chemistry students’ conceptual understanding of organic qualitative analysis. Convergent mixed methods procedure was used to collect both quantitative and qualitative data from 263 chemistry students. The 263 students were selected through multistage sampling technique to respond to organic qualitative analysis diagnostic test for students. Quantitative data was analyzed using percentages, means, and standard deviations to determine students’ level of conceptual understanding on organic qualitative analysis. The results from the study showed that, students demonstrated no scientific understanding on organic qualitative analysis. The qualitative data was open-coded and constantly compared to establish students' conceptual difficulties on organic qualitative analysis. Students demonstrated conceptual difficulties were in the form of alternative conceptions and factual difficulties. It was, therefore, recommended that chemistry teachers should select and use appropriate conceptual change instruction approaches in their teaching to help students conceptualize organic qualitative analysis contents in organic chemistry.