This study was conducted to examine the effects of practices based on the Argumentation-Based Enquiry (ABI) approach on the critical thinking of science teacher candidates in a course named the General Chemistry Laboratory course. The General Chemistry Laboratory course was taught through the ABI approach for 12 weeks, and 94 teacher candidates from three different classes participated in the study. We collected data using the Critical Thinking Test, administered at the beginning and the end of the study, and by conducting semi-structured interviews with 18 students conducted at the end of the study. The results showed that the teacher candidates who went through the ABI process experienced significant improvements in their critical thinking with regard to both skills and tendencies. In semi-structured interviews, prospective teachers stated that the stages within the ABI approach allowed them to think critically and supported the development of critical thinking.