Background: Hypertension and diabetes, key risk factors for cardiovascular disease, are significant health problems globally. As cardiovascular disease is one of the leading causes of mortality in Mongolia since 2000, clinical guidelines on arterial hypertension and diabetes were developed and implemented in 2011. This paper explores the barriers and enablers influencing the implementation of these guidelines in the primary care setting. Methods: A phenomenological qualitative study with semi-structured interviews was conducted to explore the implementation of the diabetes and hypertension guidelines at the primary care level, as well as to gain insight into how practitioners view the usability and practicality of the guidelines. Ten family health centres were randomly chosen from a list of all the family health centres (n = 136) located in Ulaanbaatar City. In each centre, a focus group discussion with nurses (n = 20) and individual interviews with practice doctors (n = 10) and practice managers (n = 10) were conducted. Data was analysed using a thematic approach utilising the Theoretical Domains Framework. Results: The majority of the study participants reported being aware of the guidelines and that they had incorporated them into their daily practice. They also reported having attended guideline training sessions which were focused on practice skill development. The majority of participants expressed satisfaction with the wide range of resources that had been supplied to them by the Mongolian Government to assist with the implementation of the guidelines. The resources, supplied from 2011 onwards, included screening devices, equipment for blood tests, medications and educational materials. Other enablers were the participants commitment and passion for guideline implementation and their belief in the simplicity and practicality of the guidelines. Primary care providers reported a number of challenges in implementing the guidelines, including frustration caused by increased workload and long waiting times, time constraints, difficulties with conflicting tasks and low patient health literacy. Conclusions: This study provides evidence that comprehensive and rigorous dissemination and implementation strategies increase the likelihood of successful implementation of new guidelines in low resource primary care settings. It also offers some key lessons that might be carefully considered when other evidence-based clinical guidelines are to be put into effect in low resource settings and elsewhere.