BACKGROUND: Smoking, physical inactivity, low fruit and vegetable consumption, and obesity are common in Kosovo. Their prevention is a priority to relieve the health system of from costly non-communicable disease treatments. The Accessible Quality Healthcare project is implementing a primary healthcare intervention that entails nurse-guided motivational counselling to facilitate change in the domains of smoking, diet, alcohol consumption and physical inactivity for at-risk patients. This study quantitatively assesses the uptake of motivational counselling and the distribution of health behaviours and stages of health behaviour change of the participants according to the intervention, as well as qualitatively describes experiences and perceived benefits of motivational counselling. METHODS: Study participants (n = 907) were recruited consecutively in 2019 from patients visiting the Main Family Medical Centres in 12 municipalities participating in the Kosovo Non-Communicable Disease Cohort study as part of the Accessible Quality Healthcare project. For the quantitative study, we used baseline and first follow-up data on smoking status, physical inactivity, obesity, fruit and vegetable as well as alcohol consumption, uptake of counselling, and stages for behavioural change. For the qualitative study, in-depth interviews were conducted with a subset of 26 cohort participants who had undergone motivational counselling. RESULTS: Motivational counselling was obtained by only 22% of the eligible participants in the intervention municipalities. Unhealthy behaviours are high even in persons who underwent counselling (of whom 13% are smokers; 86% physically inactive; 93% with inadequate fruit and vegetable consumption; and 61% are obese); only the rate of smoking was lower in those who obtained counselling. Among smokers, over 80% were still in the pre-contemplation phase of behaviour change. More advanced stages of behaviour change were observed among the highly prevalent group of inactive persons and participants with poor dietary habits, among the 5 intervention municipalities. According to the qualitative study results, the participants who obtained motivational counselling were very satisfied with the services but requested additional services such as group physical activity sessions and specialized services for smoking cessation. CONCLUSIONS: More tailored and additional primary health care approaches in accordance with patients' views need to be considered for the motivational counselling intervention to reach patients and efficiently facilitate lifestyle behaviour change.