In the eastern rainforests of Madagascar, rainfed swidden rice cultivation remains prevalent despite efforts to encourage uptake of irrigated systems to reduce deforestation. We used agricultural surveys with a stratified sample of 171 households to investigate constraints on and productivity of irrigated and rainfed rice perceived by farmers, and actual rice yields. Irrigated rice plots had higher median yields (1.72 t/ha compared to 0.62 t/ha), but farmers perceived the type of rice cultivation they practised themselves as more productive, possibly reflecting differences in the land suitability, farmers experience, and other constraints. While some factors, such as pests and water, were mentioned to limit yields, access to fertiliser was not frequently mentioned by smallholders. Higher food security was related to irrigated rice farming, higher rice yields, and owning more livestock. Conservation initiatives need to target households with and without access to irrigable land to improve food security and reduce deforestation, as exclusively promoting a cessation of swidden agriculture is neglecting its cultural value and the scarcity of irrigable land in the region.