The targeted teacher profile for the 21st century includes the ability to become competent in many areas based on knowledge, skills (cognitive skills, internal skills, social skills, research skills, learning-teaching skills), and values that fit the needs of the age. This study aimed to develop, implement, and evaluate argumentation-based inquiry teaching practices for the training of qualified science teachers. In this context, first, practices in argumentation-based inquiry were developed to educate individuals with mental flexibility; the ability to look at events from different perspectives and to think in alternative ways are necessary skills for the 21st century. Second, the planned argumentation-based inquiry practices were applied for 14 weeks in the “Science Literacy” elective course. To evaluate the effect of the implementation, science teacher candidates’ scientific process skills, high-level thinking skills, and consideration of the nature of science were investigated. A “concurrent triangulation design” was used in this mixed methods research. The study group comprised 38 science teacher candidates. Quantitative data were collected using a scientific process skills test, critical thinking disposition instruments, a metacognitive awareness inventory, and a nature of science views test. Qualitative data were collected through a semi-structured interview and documents (reflective learning diaries, reflective evaluation notes). The results show that the quantitative and qualitative findings support each other. It was determined that the practices carried out during the 14 weeks contributed to the science teacher candidates’ development of scientific process skills, critical thinking tendencies, metacognitive awareness, and views about the nature of science.