Plants contain antinutritional factors (ANFs) with negative impact on protein digestibility and nutritional quality. We aim to highlight the importance of extraction method on the coextraction of different ANFs to put focus on this challenge regarding the usability of plant-protein ingredients. We mainly focus on the research behind the established, industrial techniques, wet extraction and dry fractionation, in relation to ANFs. These methods give protein powders differing considerably in protein concentrations and ANF contents. Wet extraction offers the highest protein concentration (typically >85%) and lowest ANF content (reduction between 75% and 96%, depending on the type of ANF). Usage of chemicals and energy has pushed the development of new extraction techniques; hence dry fractionation is explored. However, it was typically found that dry fractionation resulted in an accumulation of some ANFs in the resultant protein concentrates. Innovative separation methods, like selective electrodialysis, forward osmosis, immobilized metal affinity, and zinc reductants, are suggested to be effective processes for concentration, purification, and selection of proteins. In general, more research is needed, and strategies to sophisticate extraction methods, for example by combining with pre- and postprocessing, and ensure high quality of the protein fractions are mandatory.