On-farm trial dataset evaluating sweetpotato intercropped with soybean and pigeonpea under eight spatial-arrangement treatments (sole crop and 1:1 / 2:1 / row intercrop combinations), conducted with smallholder farmers in Salima and Mulanje districts, Malawi, across the 2022/2023 and 2023/2024 growing seasons. Variables include sweetpotato root count and weight (marketable and non-marketable), vine weight, soybean and pigeonpea grain yield, and partial/total Land Equivalent Ratio (LER).