Common carotid intima-media thickness (ccIMT) progression is a risk marker for cardiovascular disease (CVD), whereas healthy lifestyle habits are associated with lower ccIMT. The objective of the present study was to test whether a healthy lifestyle intervention can beneficially affect ccIMT progression. A community-based non-randomised, controlled lifestyle intervention was conducted, focusing on a predominantly plant-based diet (strongest emphasis), physical activity, stress management and social health. Assessments of ccIMT were made at baseline, 6 months and 1 year. Participants had an average age of 57 years and were recruited from the general population in rural northwest Germany (intervention: n 114; control: n 87). From baseline to 1 year, mean ccIMT significantly increased in both the intervention (0.026 [95 % CI 0.012, 0.039] mm) and control group (0.045 [95 % CI 0.033, 0.056] mm). The 1-year trajectory of mean ccIMT was lower in the intervention group (P = 0.022; adjusted for baseline). In a subgroup analysis with participants with high baseline mean ccIMT (≥0.800 mm), mean ccIMT non-significantly decreased in the intervention group (-0.016 [95 % CI -0.050, 0.017] mm; n 18) and significantly increased in the control group (0.065 [95 % CI 0.033, 0.096] mm; n 12). In the subgroup, the 1-year trajectory of mean ccIMT was significantly lower in the intervention group (between-group difference: -0.051 [95 % CI -0.075, -0.027] mm; P < 0.001; adjusted for baseline). The results indicate that healthy lifestyle changes may beneficially affect ccIMT within 1 year, particularly if baseline ccIMT is high.