Multiple forms of malnutrition coexist in Peru, especially in peri-urban areas and poor households. We investigated the magnitude of, and the contribution of, dietary and socio-demographic factors to the double burden of malnutrition (DBM) at maternal (i.e., maternal overweight/obesity with anaemia) and dyad (i.e., maternal overweight/obesity with child anaemia) levels. A cross-sectional survey was conducted among low-income mother–child (6–23 months) dyads (n = 244) from peri-urban communities in Peru. Dietary clusters and the minimum dietary diversity score (MDD) were generated for mothers and infants, respectively. A composite indicator using the maternal dietary clusters and the MDD was created to relate to dyad level DBM. Two dietary clusters were found: (i) the ‘high variety (i.e., animal-source foods, fruit and vegetables), high sugary foods/beverages’ (cluster 1) and (ii) the ‘high potato, low fruit and vegetables, low red meat’ (cluster 2). DBM prevalence among mothers and dyads was 19.9% and 36.3%, respectively. Logistic regression analyses revealed that the only socio-demographic factor positively associated with maternal DBM was maternal age (aOR/5 years: 1.35 [1.07, 1.71]). Mothers belonging to diet cluster 1 were less likely to experience the DBM (aOR = 0.52 [0.26, 1.03]), although CIs straddled the null. Socio-demographic factors positively associated with dyad level DBM included maternal age (aOR/5 years: 1.41 [1.15, 1.73]), and having ≥ two children under 5 years (aOR = 2.44 [1.23, 4.84]). Diet was not associated with dyad-level DBM. Double-duty actions that tackle the DBM are needed given that one-third of dyads and a fifth of mothers had concurrent overweight/obesity and anaemia.