Bioactive food compounds (BFCs) are micronutrients existing in small quantities in various foods. Plant, microbes, and animals are considered the main sources of bioactive components including polyphenols, flavonoids, ω-3 FAs, and so on. BFCs have many biological functions such as antioxidant, antidiabetic, antiobesity, anti-cardiovascular, anticancer, anti-inflammatory, antimicrobial, immune-modulatory, cholesterol reduction characteristics, and others. However, incorporation of BFCs in food or pharmaceutical formulations is limited because of their high liability against temperature, pH, shear, pressures, and light, as well as poor hydro-solubility in some of these compounds, low stability under human gastrointestinal conditions, and thereby lower bioavailability (BA) and reducing functional activity. Therefore, encapsulation of BFCs using micro/nanostructure systems can overcome these challenges. These encapsulation systems include nano-silver, nano-gold, nano-emulsions, liposomes, cubosomes, biopolymer-based nanoparticles, nano-gels, and so on. Finally, biopolymer-based nanoparticles and nano-gels are good choices to encapsulate the BFCs compared to other available encapsulation systems due to their advantages. Furthermore, encapsulation of BFCs in micro/nano-systems improved their bio-efficacy including antioxidant, antidiabetic, antiobesity, anti-cardiovascular, anticancer, anti-inflammatory, antimicrobial, and immune-modulatory. Among all encapsulated-BFCs, encapsulated-curcumin and -quercetin showed the highest bio-efficacy. However, further studies regarding stability, BA, and in vivo work of BFCs-loaded micro/nano-encapsulation systems are recommended to evaluate the therapeutic efficacy including physicochemical stability, target mechanisms, cellular internalization, and release kinetics.