To assess the potential industrial vegetable oil (IVO) increase made possible by SHELL DNA supply chain testing, we conducted a field survey to quantify the presence of low-yielding contaminant oil palms in smallholder plantations. In the survey, 9341 palms in 81 smallholdings in Musi Banyuasin (representing 88.8% of the total planted area) and 74 smallholdings in Pelalawan (representing 85.5% of the total planted area) were sampled and tested (planting year 2001 to 2020). Musi Banyuasin and Pelalawan regencies contained only 26.2% or 27.4% legitimate high-yielding hybrid tenera palms, respectively. The remaining 73.8% and 72.6% of palms were one of four undesirable low-yielding contaminant types. We determined that if SHELL DNA testing had been conducted in the past, smallholder FFB production (i.e., smallholder income) would have increased by 31.0% and 28.0%, PKO production would have increased by 31.0% and 28.0%, and CPO production would have increased by 49.0% and 46.0% in Musi Banyuasin and Pelalawan, respectively. We demonstrate that a ‘screen-then-plant’ paradigm for oil palm cultivation in Indonesia has the potential to improve the income of millions of Indonesian smallholders, increase the productivity of CPO and PKO mills, provide significantly increased feedstocks for biofuel conversion and further enhance the sustainability of the Indonesian palm oil industry.