Background Dietary factors seem to influence telomere length. Moreover, associations between changes in adiposity indices and telomere length (TL) have been found in intervention studies. Objective We evaluated changes in two diet quality indices and their association with TL in children with abdominal obesity in a 12-month lifestyle intervention. Methods Eighty-seven participants (7-16 years old) were assigned to the intervention (moderate hypocaloric Mediterranean diet) or usual care group (standard paediatric recommendations) for a 2-month intensive phase and a subsequent 10-month follow-up. Diet quality was assessed using the Diet Quality Index for Adolescents (DQI-A) and the Healthy Lifestyle Diet Index (HLD-I). TL was measured by monochrome multiplex real-time quantitative PCR. The intra-class correlation coefficient for TL was 0.793 (95% CI 0.707, 0.857). Results After a 12-month lifestyle intervention, a significant reduction in BMI-SDS (-0.57 and -0.49 for the intervention and usual care groups, respectively) and fat mass was observed in all subjects without differences between groups. Changes in DQI-A (+12.36% vs +5.53%,P= .005) and HLD-I (+4.43 vs +1.09,P < .001) were higher in the intervention subjects compared with usual care subjects after 2 months. Interestingly, we observed a positive change in TL between 2 and 12 months (P= .025), which was associated with higher scores on the DQI-A (beta= 0.008,R-2= 0.088,P= .010) and HLD-I (beta= 0.022,R-2= 0.198,P= .015), in the intervention group after the 2-month intensive phase. Conclusion Favourable changes in diet quality indices could contribute to telomere integrity in children with abdominal obesity enrolled in an intensive lifestyle intervention.