The manufacturing of human mesenchymal stem cells (hMSCs) as cell-based products for clinical use should be performed with appropriate controls that ensure its safety and quality. The use of hMSCs in cell therapy has increased considerably in the past few years. In line with this, the assessment and management of contamination risks by microbial agents that could affect the quality of cells and the safety of patients have to be considered. It is necessary to implant a quality control program (QCP) covering the entire procedure of the ex vivo expansion, from the source of cells, starting materials, and reagents, such as intermediate products, to the final cellular medicine. We defined a QCP to detect microbiological contamination during manufacturing of autologous hMSCs for clinical application. The methods used include sterility test, Gram stain, detection of mycoplasma, endotoxin assay, and microbiological monitoring in process according to the European Pharmacopoeia (Ph. Eur.) and each analytical technique was validated in accordance with three different cell cultures. Results showed no microbiological contamination in any phases of the cultures, meeting all the acceptance criteria for sterility test, detection of mycoplasma and endotoxin, and environmental and staff monitoring. Each analytical technique was validated demonstrating the sensitivity, limit of detection, and robustness of the method. The quality and safety of MSCs must be controlled to ensure their final use in patients. The evaluation of the proposed QCP revealed satisfactory results in order to standardize this procedure for clinical use of cells.