Background: Regular physical activity is essential for metabolic control in type 2 diabetes mellitus. Aims: The aim of this study was to assess the short and long-term impact of a multifactorial intervention on physical activity and clinically relevant biochemical parameters in patients with type 2 diabetes mellitus. Methods: This randomised, controlled clinical trial (NCT02991079) included two parallel groups aged 25–70 years from a primary care health centre in Salamanca, Spain. The subjects were assigned randomly (1:1) to control and intervention groups, using Epidat 4.0 software. Both were counselled on the importance of physical activity and maintaining a healthy diet. The intervention group also took five low–moderate intensity 4 km nurse-guided walks, received a smartphone application to promote healthy habits and attended a diet workshop. Physical activity was measured objectively using a pedometer and subjectively using a shortened international physical activity questionnaire (at baseline, 3 and 12 months). Results: In total, 204 subjects were included (mean age 60.6 years, 45.6% were women). After 3 months, relative to the control group, the intervention group increased their daily number of steps by 1852, aerobic steps by 1623, distance walked by 994 m, and total metabolic equivalent minutes per week by 1297 and decreased sedentary time by 34.3 minutes per day. Differences from baseline persisted at 12 months, including mean increases of 1141 daily steps, 917 aerobic steps, and 1065 total metabolic equivalent minutes per week in the intervention group relative to the control group ( P<0.05 for all). Conclusions: The success of this multifactorial intervention should help inform future clinical approaches and application designs towards managing type 2 diabetes mellitus and improving patient outcomes.