Abstract Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.