The immune system is somehow related to all the metabolic pathways, in a bidirectional way, and the nutritional interventions affecting these pathways might have a relevant impact on the inflammatory status of the individuals. Food-derived peptides have been demonstrated to exert several bioactivities by in vitro or animal studies. Their potential to be used as functional food is promising, considering the simplicity of their production and the high value of the products obtained. However, the number of human studies performed until now to demonstrate effects in vivo is still scarce. Several factors must be taken into consideration to carry out a high-quality human study to demonstrate immunomodulatory-promoting properties of a test item. This review aims to summarize the recent human studies published in which the purpose was to demonstrate bioactivity of protein hydrolysates, highlighting the main results and the limitations that can restrict the relevance of the studies. Results collected are promising, although in some studies, physiological changes could not be observed. When responses were observed, they sometimes did not refer to relevant parameters and the immunomodulatory properties could not be clearly established with the current evidence. Well-designed clinical trials are needed in order to evaluate the role of protein hydrolysates in immunonutrition.