Aims: We hypothesised that the expected increase in insulin resistance over three years’ time in individuals with impaired glucose tolerance (IGT) and/or impaired fasting glucose could be attenuated by an intervention with focus on physical activity in ordinary primary care. Methods: We conducted a randomised controlled trial with 96 participants over three years. Examination of the participants included anthropometric measures, blood pressure, body weight and height, blood samples, an oral glucose tolerance test, and questionnaires about diet and lifestyle. The study subjects were randomised to either an intense intervention with information, group sessions, referral to physical activity and a step-counter (n = 31), a less intense intervention without the group sessions (n = 35), or care as usual group (CAUG) (n = 30). Differences between the groups were analysed with general linear models adjusted for age, gender, baseline values and time in the intervention. Results: Individual insulin resistance increased in the CAUG. Due to having a similar effect, we combined the two intervention groups into a combined intervention group (CIG; n = 66) in the analyses. In individuals with IGT, the increase in the homeostatic model assessment-insulin resistance differed significantly between those in the CAUG and the CIG ( = 0.8; CI: 0.1–1.6; p = 0.034). Likewise, diastolic blood pressure decreased more in the CIG than in the CAUG ( = 5.1; CI: 0.1–10.0; p = 0.047). A total of 17 individuals developed Type 2 diabetes, 23% were in the CIG and 33% in the CAUG; so there was a 32% reduced risk in the intervention group. Conclusions: A lifestyle intervention focused on physical activity is feasible in ordinary primary care and prevents deterioration in insulin sensitivity in individuals with IGT over a three-year period.