The production of recombinant molecules in seeds plant has presented interesting results related to the synthesis, secretion, compartmentalisation, post-translational modifications and purification, scalability, stable expression, the absence of contaminants and human pathogens, and knowledge of the growth, harvest, storage and processing practices. In this context, the soybean plant has emerged as an option to express recombinant proteins. We obtained several transgenic soybean plant lines, expressing different types of recombinant molecules, under the control of the tissue-specific soybean seed storage β-conglycinin promoter. This promoter is the most abundant protein in soybean seeds, directing the expression of the molecules that accumulate in the seed storage tissue. Cotyledonary immunocytochemical analysis of the seeds demonstrated that the targeted proteins effectively drove polypeptide accumulation into the protein storage vacuoles (PSVs). Here, we provide a detailed protocol to reproduce the results described above and properly direct the expression of recombinant protein into the PSVs.