The distribution of printed materials is the most frequently used strategy to disseminate and implement clinical practice guidelines, although several studies have shown that the effectiveness of this approach is modest at best. Nevertheless, there is insufficient evidence to support the use of other strategies. Recent research has shown that the use of computerized decision support presents a promising approach to address some aspects of this problem.The aim of this study is to provide qualitative evidence on the potential effect of mobile decision support systems to facilitate the implementation of evidence-based recommendations included in clinical practice guidelines.We will conduct a qualitative study with two arms to compare the experience of primary care physicians while they try to implement an evidence-based recommendation in their clinical practice. In the first arm, we will provide participants with a printout of the guideline article containing the recommendation, while in the second arm, we will provide participants with a mobile app developed after formalizing the recommendation text into a clinical algorithm. Data will be collected using semistructured and open interviews to explore aspects of behavioral change and technology acceptance involved in the implementation process. The analysis will be comprised of two phases. During the first phase, we will conduct a template analysis to identify barriers and facilitators in each scenario. Then, during the second phase, we will contrast the findings from each arm to propose hypotheses about the potential impact of the system.We have formalized the narrative in the recommendation into a clinical algorithm and have developed a mobile app. Data collection is expected to occur during 2018, with the first phase of analysis running in parallel. The second phase is scheduled to conclude in July 2019.Our study will further the understanding of the role of mobile decision support systems in the implementation of clinical practice guidelines. Furthermore, we will provide qualitative evidence to aid decisions made by low- and middle-income countries' ministries of health about investments in these technologies.