The use of new, alternative sources for protein has led to a new (potential) portfolio of protein isolates. However, information on the exact composition of these protein products is limited, especially on the minor components present. Hence, the evaluation of the relationships between minor components and proteins including both physical (technical functionality) and biological functions (digestibility, nutritional, sensory and food safety) needs to be investigated. Minor components can be either naturally present, present due to contamination or formed during the technological processing to protein fractions. Negative effects could include reduced protein digestibility, undesired colouring or off-flavour. On the other hand, these same compounds may have protective effects on physiological and biological properties. We aim to get insight into these type of effects, come to processing routes to reduce negative effects and enhance positive effects of these minor components in current and future protein products. Included protein sources are among others faba beans, peas, soybeans and sunflower seeds and canola seeds. Via a literature study and expert interviews, we set out to obtain a list of minor components expected to be either naturally present or formed during processing of these selected protein sources. This includes an indication of their presumed positive and negative effects on human and animal health and protein functionality. Suggested alternative processing techniques tested and evaluated. Technical protein functionality will also be assessed by looking at gelation properties, while the nutritional aspects will be assessed by looking at protein digestibility. The results of this work are valuable for future researchers in the field of alternative protein sources, industrial players and consumers. It will enable improved industrial production of protein isolates adjusted to consumer’s needs.