Greenhouse cultivation is highly efficient in the use of water and fertilizers. However, due to intensive production, the greenhouse industry applies ample amounts of water and fertilizers. An alternative to minimize water and nutrient loss is zero-leaching systems, such as closed-loop subirrigation. The objective of the present study was to compare the water and fertilizer use efficiency in containerized tomato plants grown in a subirrigation system and a drip irrigation system. Subirrigated plants exhibited lower biomass than drip-irrigated plants. However, the amount of nutrient solution required to restore evapotranspirated water was lower in subirrigation. The yield was marginally decreased in subirrigated plants compared to drip-irrigated plants. The amount of nutrient solution required to produce 1 kg of fresh tomatoes was 22 L in subirrigation, whereas in drip irrigation, plants demanded 41 L. The total nitrogen applied through the nutrient solution was 75% lower in subirrigation than in drip irrigation, while the phosphorus, potassium, calcium and magnesium applied was 66%, 59%, 70% and 74% lower, respectively. We concluded that the subirrigation system proved to be more water- and nutrient-efficient than the drip irrigation system due to the zero leaching of the nutrient solution, the lower number of irrigation events required and the lower nutrient demand of plants.