Background: This study aims to evaluate trends of DBM in Peru over the last 20 years. Methods: Using individual-level data collected in nationally representative household surveys from Peru between 1996 and 2017, we analysed trends in the prevalence and patterning of the DBM. We classified the nutritional status of children and their mothers as undernourished (either underweight, stunted or wasted for children), normal, overweight or obese. Children classified as experiencing the DBM were those undernourished and living with an overweight or obese mother. We also fitted logistic regression models to evaluate the probability of children having an overweight/obese mother across subgroups of socioeconomic status, place of residence and education. Results: The overall percentage of children experiencing the DBM in 2016 was 7%, and constitutes ~203,600 children (90% of whom were stunted). Between 1996 and 2016, undernourished children have seen the largest relative increase in the risk of having an overweight mother (31% vs. 37%) or obese mother (6% vs. 17%); however, due to the substantial decrease in the absolute number of undernourished children, the DBM has not grown. Moreover, all children, irrespective of their own nutritional status, are now more likely to live with an overweight or obese mother, a consistent pattern across wealth, location and education subgroups, and all regions of Peru. Conclusions: DBM prevalence in Peru has decreased, although the number of DBM cases is estimated to be above 200,000. In addition, all children are now more likely to live with overweight or obese mothers. The basic pattern has shifted from one of undernourished children whose mothers have a ‘normal’ BMI, to one where now most children have a ‘normal’ or healthy anthropometric status, but whose mothers are overweight or obese. This suggest that Peru is on the cusp of a major public health challenge requiring significant action.