This study aimed to explore whether maternal food and nutrition literacy (FNL) can mitigate negative effects of food insecurity on children's eating habits and assist food-insecure households in making better nutrition choices with limited resources available. A cross-sectional study was conducted on children aged 6 to 12 years and their mothers. FNL was assessed using a validated Food and Nutrition Literacy Assessment Tool, and household food security was evaluated with the Household Food Insecurity Access Scale. Eating habits were measured through a structured questionnaire that focused on various dietary habits. Logistic regression was used to determine the associations between maternal FNL, food insecurity status, and children's eating habits. A total of 327 children-mothers, comprising 159 food-secure and 168 food-insecure households, were evaluated. Maternal FNL was inversely associated with consumption of fast-foods and fried foods, and skipping breakfast in both food-secure and food-insecure participants. However, only food-secure participants showed an inverse association between FNL and the habit of eating out. Both groups indicated lower sweet consumption associated with higher FNL. Maternal FNL was inversely associated with lower dairy and nut intake in food-secure group and lower fruit and vegetable consumption in food-insecure participants. This study suggests that in conditions of food insecurity FNL may reduce the negative impact of food insecurity on children's nutrition choices and food habits.