The purpose of this study was to investigate the effectiveness of explicit-embedded-reflective (EER) instruction in scientific literacy levels of the ninth grade advanced science students by assessing content knowledge and scientific literacy levels. The study was conducted with 51 students by using experimental design. In the treatment group, the EER teaching was performed, while in the comparison group the instruction was conducted by lecturing, demonstration and questioning strategies in a teacher-centred context. Nature of Science Literacy Test and Cell Content Knowledge Test were used for data collection. T-tests were utilized for data analysis. The results of the study showed that the EER teaching was effective in terms of increase in scientific literacy levels and cell content knowledge in the treatment group. In addition, the approach was more effective in increasing scientific literacy levels and cell content knowledge than the regular approach.