Food is inextricably linked to human health and environmental sustainability; however, very little is known about children’s perceptions of the concept of sustainability in the context of food choices. We aimed to explore the perceptions of Chilean schoolchildren about environmental sustainability, food, and nutrition. Eight online focus groups were conducted with boys and girls aged 8–9 (n = 30). Questions related to environmental sustainability, pocket money, and food characteristics such as price, front-of-package (FOP) warning label, and eco-labels were included. Data analysis was conducted using ATLAS.ti through a hybrid content analysis approach. Five central themes were identified: (1) children’s favorite snacks, (2) knowledge of sustainability, (3) sustainability and eco-labels use, (4) healthfulness of food products, and (5) pocket money and food prices. Most children were not aware of the meaning of “environmental sustainability”, but the concept was understood when it was explained in plain language. Participants showed awareness about the environmental impact of their eating behavior, had a positive perception of eco-labels, and identified food with fewer warning labels as “better” options. Results indicate that children understand the concept of sustainability in food if it is communicated clearly, and that eco-labels may be an effective tool in that effort.