Aqueous fractionation of protein from lupin seeds was investigated as an alternative to the conventional wet fractionation processes, which make use of organic solvents. The effect of extraction temperature was studied and the consequences for downstream processing were analysed. Omitting the extraction of oil with organic solvents resulted in a protein isolate that contained 0.02–0.07goilg−1 protein isolate, depending on the exact extraction conditions. Nevertheless, the protein functionality of the aqueous fractionated lupin protein isolate was similar to the conventional lupin protein isolate. The protein isolate suspension could be concentrated to 0.25gmL−1 using ultrafiltration, which provides a relevant concentration for a range of high-protein products. Based on the results, we conclude that aqueous fractionation can be a method to lower the environmental impact of the extraction of proteins from legumes that contain water- and dilute salt-soluble proteins.