In this research, a novel methodology based on the simulation of a call for research projects was applied for the training of STEM secondary school teachers, with results raised and analyzed to determine the response of the students to this new methodology. The activity was applied in the same course during two academic years with student groups from very different teaching specialties such as mathematics, physics and chemistry, biology and geology, technology and health processes who were studying the Master’s Degree in Secondary Education, specifically, the 3 European Credit Transfer and Accumulation System (ECTS) course of Initiation to Educational Research (IER), this Master’s course being mandatory for working as a secondary professor. The Master’s students are asked to write their own research project proposals for a fictitious call on a topic freely chosen by them, which might have been related to the research line of the final Master’s thesis. In it, they had to propose all the contents studied in the course (such as writing a brief state of the art, establishing a research team, setting objectives, a description of the methodology for educational research, instruments, a plan for the dissemination of the results, the needed resources, etc.). The students’ perceptions of the usefulness and reality of what they had learned for their professional development and for writing their final theses were assessed. The results based on the perceptions of the students demonstrate that the activity had been useful for assimilating concepts related to educational research in the context of secondary education (research skills), which will be useful for improving the critical sense of the students (teacher candidates) and for their professional future in the context of applied research in day-to-day secondary teacher activities. Furthermore, the results show the activity was useful for the development of the final Master’s thesis. The difficult aspects that the activity presented for them were analyzed. The results were statistically compared for the students of the different specialties, deducing, in all cases, a homogeneous good acceptance with slight differences between them.