Childhood under‐nutrition and malnutrition are prevalent in low and middle‐income countries. Where agriculture is the primary source of food production, consumption, and cash income, it has a close relationship with health and nutrition in these emerging economies. Although Timor‐Leste achieved lower middle‐income status in 2011, national economic growth has not delivered anticipated nutritional dividends. Seeking to redress a lack of research that clearly demonstrates how agriculture impacts on nutrition in Timor‐Leste, we investigated the links between household agricultural activities and children's physical growth in two agro‐ecologically varying field sites: lowland Natarbora and mountainous Ossu. Children in both sites were below World Health Organization standards in height, weight, and body mass index. Coastal children recorded better growth than upland children. Livestock production was linked to poorer growth in the upland, but not coastal communities, which may be linked to specific differences in husbandry practices. In both communities, access to a plantation was somewhat associated with children's (0–10 years) increased weight‐for‐age. As simple agricultural indicators do not fully explain growth outcomes, a livelihood security approach is proposed to better understand how households address food and nutritional needs in relation to broader livelihood concerns.