In an evolving perspective, lecturers consider that inquiry is one of the best forms of learning to drill critical thinking. This study assesses the practice of inquiry to develop the critical thinking skills of prospective science, technology, engineering, and mathematics (STEM) teachers in Indonesia, which is a suitable way to address the problems in the country. Through the experimental design, three groups were formed, which were intervened with inquiry learning, inquiry-creative, and traditional teaching. The learning intervention was carried out within one month using a pre-validated instrument. The critical thinking data were analyzed descriptively based on the pre-test and post-test mean parameters and n-gain on critical thinking indicators, as well as individual critical thinking performance. Statistical analyses (paired-t test, ANOVA, and least significant difference test) were employed to provide confidence in the differences in critical thinking skills across the three learning treatments (p < 0.05). The prospective STEM teachers’ critical thinking skills showed varied performances among the three groups. The inquiry-creative group had the strongest impact, followed by inquiry and traditional teaching, all differing significantly. In summary, the findings suggest that current teaching practices in STEM education need to be reconsidered, showing the advantage of the inquiry-creative model in developing the critical thinking skills essential for future teachers and creators in the STEM fields.