Abstract The study aims to explore the implementation of stepwise inquiry in chemistry education. The levels of inquiry used range from structured inquiry (level 1) to guided inquiry (level 2). The research design involved methods of analyzing the implementation of inquiry levels, assessing the ability to answer questions, engage in critical thinking, and gather student responses. The research sample consisted of 73 students studying biochemistry. A total of 14 groups, each containing 5–6 members, were involved in this research. The research results show that six groups (SG) successfully followed the investigation process at the inquiry steps, while eight groups were unsuccessful (UG). The average scores of the sub-skills collaboration, communication, data collection, use of equipment, and implementation of experimental design were the highest compared to other subskills. The stages of interpreting problems, observation, experimental design, formulating hypotheses, data analysis, and developing conclusions are still in progress and are classified as low. The SG group had an average N-Gain critical thinking score higher than the UG group (p < 0.05). The analysis of the ability to answer questions and think critically shows that the category of developing hypotheses and analyzing arguments had the lowest ability to respond compared to other indicators.