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Background: A sizable cross-sectional studies demonstrated a low dietary diversity in Southern Ethiopia. However, its seasonal trend has not been well studied in areas where nutrient-poor enset (false banana (Ensete ventricosum)) foods are major staple. Moreover, there is scarcity of information on seasonal nature of anthropometric status of mother–child pairs (MCP) from the same areas in Southern Ethiopia. Therefore, the present study aimed to investigate the dietary diversity and anthropometric status of MCP in postharvest dry and lean wet seasons and identify factors associated with anthropometric status. Methods: The dietary intake and anthropometric data were collected from 578 households (578 mothers and 578 children) January–June 2017. The study compared data of the two seasons using McNemar’s test for dichotomous, Wilcoxon signed-rank test for non-normally distributed, and paired samples t-test for normally distributed continuous data. Logistic regression was conducted to identify risk factors for malnutrition. In addition, Spearman’s Rho test was used to determine correlations between maternal and child variables. Results: Over 94% of the mothers did not fulfil the minimum diet diversity score in both seasons. The meal frequency and pulses/legumes intake significantly declined in lean wet season; however, dark green leaves consumption increased. Meat, poultry, and fish consumption dropped to almost zero in the lean wet season. The dietary diversity and anthropometric status of the MCP were correlated. Weight-for-age (WAZ) and weight-for-height (WHZ) of children significantly declined in the lean wet season. In the same way, maternal mid upper arm circumference (MUAC), body weight, and body mass index (BMI) dropped (p < 0.001) in this season. Being pregnant and a lactating mother, poverty, and the ability to make decisions independently predicted maternal undernutrition (low MUAC). On the other hand, maternal undernutrition and education were associated with child underweight. Conclusions: The results demonstrated that the dietary diversity of MCP is low in both postharvest dry and lean wet seasons. This suggests the need for continuous nutrition intervention to improve the dietary diversity. In addition, the anthropometric status of MCP declines in lean wet season. This may provide some clue for policy targeting on improving nutritional status of mothers and children in rural Southern Ethiopia. Full article