Objectives Analysing data of the Young Lives Study in Peru, we aimed at assessing the association between daily food frequency and body mass index (BMI) changes between 2006 and 2016.

Design Secondary analysis of a prospective ongoing cohort study.

Setting 20 sentinel sites in Peru.

Participants Children enrolled in the younger cohort of the Young Lives Study. We used information from the second (2006–2007), third (2009–2010), fourth (2013–2014) and fifth (2016–2017) rounds of the younger cohort in Peru.

Primary and secondary outcomes BMI as well as BMI-for-age z-score, both as numerical variables.

Results Data from 1948 children, mean age 4.3 (SD: 0.3) years and 966 (49.6%) women were included at baseline. In multivariable model, lower food consumption frequency was associated with increased BMI and BMI-for-age z-scores: children reporting <4 times of food consumption per day had a greater increase in BMI (β=0.39; 95% CI 0.17 to 0.62) and BMI-for-age z-score (β=0.07; 95% CI 0.01 to 0.13) compared with those reporting 5 per day. Results were consistent for those reporting exactly eating 4 times per day (β for BMI=0.16; 95% CI 0.02 to 0.30 and β for BMI-for-age z-score=0.05; 95% CI 0.01 to 0.09).

Conclusions Children who eat <5 times per day, gain more BMI compared with those who eat ≥5 times. Parents should receive information to secure adequate nutrition for their children, both in terms of quality and quantity.