This paper uses a directional distance function and a single truncated bootstrap approach to investigate inefficiency of lowland farming systems in the Benin Republic. First, we employed a dual approach to estimate and decompose short-run profit inefficiency of each farming system into pure technical, allocative and scale inefficiency and also into input and output inefficiency. Second, an econometric analysis of factors affecting the inefficiency was generated using a single truncated bootstrap procedure to improve inefficiency analysis statistically and obtain consistent estimates. In the short run, scale, allocative and output inefficiency were found to be the main sources of inefficiency. Based on inefficiency results, the inefficiency of lowland farming systems is the most diverse. Compared to a vegetable farming system, technical inefficiency is significantly higher if farmers switch to a rice farming system. Scale, allocative, output, and input inefficiency are significantly lower with an integrated ricevegetable farming system and there was high prevalence of increasing returns to scale in the integrated rice-vegetable farming system. Water control and lowland farming systems are complements and play a significant role in the level of inefficiency. Input inefficiency shows the difficulty that the producers face in adjusting the quality and quantity of seeds and fertilizers. The paper provides empirical support for efforts to promote an integrated rice-vegetable farming system in West Africa lowlands to increase food security.