Various environmental, food security and population health problems have been correlated with the use of intensive agriculture production systems around the world. This type of system leads to the loss of biodiversity and natural habitats, high usage rates of agrochemicals and natural resources, and affects soil composition, human health, and nutritional plant quality in rural areas. Agroecological intercropping systems that respect agrobiodiversity, on the other hand, can significantly benefit ecosystems, human health, and food security by modifying the nutritional profile and content of some health-promoting bioactive compounds in the species cultivated in this system. However, research on intercropping strategies focuses more on the benefits they can offer to ecosystems, and less on plant nutrient composition, and the existing information is scattered. The topic merits further study, given the critical impact that it could have on human nutrition. The aim of this review is therefore to collect viable details on the status of research into the profile of nutrients and bioactive compounds in intercropping systems in different regions of the world with unique mixed crops using plant species, along with the criteria for combining them, as well as the nutrients and bioactive compounds analyzed, to exemplify the possible contributions of intercropping systems to food availability and quality.