Molecular cloning skills are an essential component of biological research, yet students often do not receive this training during their undergraduate studies. This can be attributed to the complexities of the cloning process, which may require many weeks of progressive design and experimentation. To address this issue, we incorporated an immersive 12-week undergraduate research experience into an upper-level molecular microbiology course. Students completed two 6-week modules where the entire molecular cloning process was carried out for two sets of novel genes implicated in distinct biological processes, microbial cell division and bacterial pathogenesis. The first module trained students in molecular cloning experimental skills, and the second facilitated the application of these skills within a new biological context. Students designed and optimized primers targeted against specific genes, and then PCR amplified, purified, and quantified the DNA of their gene of interest. Using a variety of strategies, students inserted these genes into expression plasmids to produce GFP and His-tag fusion proteins; this was tested through restriction digestion or colony PCR and verified by gel electrophoresis. At the end of each module, students were assessed on comprehension of biological concepts, professional laboratory note-keeping and scientific communication, and proficiencies in experimental procedures. The recombinant plasmids produced by the students directly contributed to ongoing research projects, and the molecular cloning skills learnt are applicable to many career and study options in molecular biology. Overall, this research experience trained students in professional molecular biology and microbiology practice and engages them in producing real-world research outcomes.