Background: Drugs with fiscalized substances without a correct prescription may lead to undesirable side effects. Pharmacy staff needs to improve their competencies (knowledge, skills, and attitudes) to contribute to providing ambulatory pharmacy services and minimizing medication errors. Continuing education programs (CEP) could favor access to relevant and quality information on health promotion, disease prevention, and the rational use of drugs. Objective: To evaluate the effectiveness of a continuing education program to improve pharmacy staff competencies to enhance the use of drugs with fiscalized substances. Methods: A multicenter, prospective, parallel-group, cluster-randomized, controlled clinical trial was conducted in drugstores and pharmacies in Colombia (ambulatory retail establishments). The intervention group (IG) received a CEP: a web-based social networking site, a virtual course, a dispensing information system, and face-to-face training. The control group (CG) received general written material on the correct use of drugs. We measured pharmacy staff's skills, attitudes, and knowledge self-reported scores, and the simulated patient technique was used to assess the participant skills and attitudes in real practice. We used a questionnaire designed for this study, which was evaluated by a group of experts and piloted and showed a Cronbach's alpha of 0.96. Results: Three hundred five drugstores and pharmacies were enrolled in two groups: IG (n = 153) and CG (n = 152). Out of the 750 potential participants, 88% (n=659) agreed to participate. The pharmacy staff's skills, attitudes, and knowledge self-reported scores post-intervention were higher than baseline in both groups; however, the IG had statistically significantly higher scores than the CG. Post-intervention, the self-efficacy skills and attitudes in the IG improved by 88% (22 of 25) and in six of the seven assessed knowledge components (p<0.001). However, the dispensing criteria evaluated with simulated patient methodology showed no statistically significant differences between groups in the pharmacy staff's skills and attitudes in real practice. Conclusions: Providing a continuing education program using different educational strategies improved the pharmacy staff's competencies (assessed knowledge and self-reported skills and attitudes) to enhance the use of drugs with fiscalized substances. However, there were no improvements in skills and attitudes in real practice. These findings could show that pharmacy staff needs additional and continuous training/sustainability.