In Indonesia more than 40% of the area under oil palm is owned by smallholders. The productivity in smallholder plantations is usually less than in large plantations, and limited fertiliser applications may be one of the key reasons. We investigated the use of fertilisers by > 300 smallholder farmers in Sumatra and Kalimantan, some of whom were involved in training programmes aimed at yield improvement. In our sample, the total applications of N were largest (166 kg ha−1 year−1), followed by K (122 kg) and P (56 kg). The applications of K were insufficient to compensate for the off-take with a production of 20 tonne fruit bunches ha−1 year−1, while N applications were excessive. On average, farmers applied 1130 kg fertiliser ha−1 year−1, and relied strongly on subsidised fertilisers, especially NPK Ponska (66%) and urea (39%). The average costs for fertiliser application were USD 225 ha−1 year−1. Trained farmers applied significantly more P in one research area, but for the other nutrients and research areas, there was no significant difference between trained and untrained farmers. Plantation size and nutrient application were weakly correlated in some areas, but not in the sample as a whole. Previously reported nutrient application rates were mostly less than our findings indicated, suggesting that actual nutrient limitations may be more severe. To overcome nutrient limitations and enhance nutrient use efficiency, we recommend that fertilisers are used in the correct balance; a ground cover vegetation is maintained to protect against erosion; and the application of empty fruit bunches is encouraged.