Patient safety and quality of care are fundamental pillars in the health policies of various governments and international organizations. The purpose of this study is to evaluate nurses’ perceptions on the degree of implementation of a protocol for the standardization of care and to measure its influence on notification of adverse events related to the administration of medications. This comparative study used data obtained from questionnaires completed by 180 nurses from medical and surgical units. Our analyses included analysis of variance and regression models. We observe that the responses changed unevenly over time in each group, finding significant differences in all comparisons. The mean response rating was increased at 6 months in the intervention group, and this level was maintained at 12 months. With the new protocol, a total of 246 adverse events and 481 incidents without harm was reported. Thus, actions such as the use of protocols and event notification systems should be implemented to improve quality of care and patient safety.