Various environmental, food security and population health problems seem to be related to intensive agriculture production worldwide. This type of food production system impacted the loss of biodiversity and natural habitats; high usage rates of agrochemicals and natural resources had affected soil composition, human health, and nutritional plant quality in rural areas. Intercropping agroecological systems that respect agrobiodiversity could significantly benefit ecosystems, human health, and food security by modifying the nutritional profile and the content of some health-promoting bioactive compounds of the species cultivated in this system. Research on intercropping strategies focuses on the benefits they can offer to ecosystems and less on nutrient plant composition, leaving information scattered when this theme should be more studied due to the critical impact it could provide for human nutrition. Therefore, this review aims to collect viable details on the investigation status of nutrients and bioactive compounds profile in intercropping systems by verifying 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 show what intercropping systems can contribute to food availability and quality.