The reprocessing of medical devices is a practice that, over the years, has become well accepted in the area of health care. However, to carry out this process focusing on the safety of the patient and the environment, it is necessary to have standardized practices. The goal of this paper is to propose a standardization protocol for the use and reprocessing of medical devices, that considers all the life cycle stages in which the entity in charge of using the medical device is involved in, that is, from the acquisition to the final disposal of the device, in order to have an adequate traceability of the process. This protocol was constructed with a qualitative approach and validated through an emulation applied in a Metrosalud medical center, in Medellín. A properly structured protocol for the use and reprocessing of medical devices improves patient care and protects the environment by reducing hospital waste and the associated economic costs.