Preliminary research shows the difficulties of students in understanding the concepts of photosynthesis and cellular respiration which is characterized by the low achievement of student learning outcomes in the academic field. This research is based on the desire of researchers to find out the factors that influence student’s learning difficulties, namely factors of misconception or low mastery of concepts by students. This study used a pre-experiment with a one group pre-test post-test design approach. The research instruments consisted of subtopic biology Photosynthesis and Cellular Respiration modules, RPP, instruments for identifying student misconceptions, concept mastery test instruments, and science process skills test instruments (KPS). The study population was students of class XII of the SMA Negeri 2 Palangkaraya Science Department with the research sample being Class 12 IPA-8 which amounted to 41 students. The procedure of data collection is taken using 2 types of data, namely using multiple-choice questions (three-tier multiple tests) to identify misconceptions and questions in the form of descriptions for mastery of concepts and KPS. Analysis of pre-test and post-test data using the Certainty of Response Index (CRI) method. The results showed the level of student misconception before being given scientific literacy-based learning was quite high with a percentage of 68.29%. Another impact of the application of scientific literacy-based learning strategies to the achievement of student learning outcomes is increasing the ability to master student concepts and science process skills (KPS) in the subtopics of photosynthesis and cellular respiration.