Studies have shown that many students do not attain the subject-specific proficiency required in chemistry classes; therefore, their basic knowledge of chemistry is lacking. However, this deficit cannot easily be compensated for in the further years of learning because of the hierarchical structure of chemistry as a subject. To support cumulative teaching and learning, this study developed a learning progression for the beginning of chemistry instruction in close collaboration with school practice. This study focused on core ideas, which are fundamental chemistry concepts logically linked in a strand map. This study investigated the dependence of the understanding of one core idea on that of another to empirically validate possible learning pathways. Subject knowledge items were developed for each core idea, piloted, and administered to students in the first 3 years of learning at the lower secondary level in a quasi-longitudinal study combined with a true longitudinal study. The quality of the subject knowledge test was satisfactory, as determined using item response theory models. Many of the hypothesized dependencies were confirmed using the McNemar test. Simultaneously, students were shown to have low knowledge relative to curricular specifications.