The applications of solid lipid nanoparticles (SLN) and nanostructured lipid carrier (NLC) might be reduced because of entrapment efficiency, rate of sustained drug release and drug explosion in matrix systems over storage time in food model system and human's gastrointestinal tract. Present review discusses that encapsulation matrices have to be manipulated concerning different manufacturing methods, including cysteinefunctionalized NLCs and SLNs, hydrophobic ion pairing, and co-polymer with positively charged polymer and the nano lipid compositions, mainly cationic surfactant and penetrations. Modifying matrices not only protects encapsulated ingredients against chemical degradation and provides maximal physical stability but also allows for precise control release and augments anti-microbial targets in food and pharmaceutical applications. Antimicrobial compounds-loaded cationic SLNs and NLCs could prolong their antibacterial activity to days and months which may be attributed to the controlled release of bio-active compounds from the nano-capsules. Nano particles' antibacterial efficacy against various Gram-positive and negative species increased in positively and neutrally charged nanoparticles than in negatively nanoparticles. Moreover, modification of SLNs and NLCs provide the opportunity to decrease resistance of biofilm's infections against anti-microbial components, causing efficiently anti-microbial activity and inhibiting the overuse of antibiotic consumptions. Nano-roughness of SLNs or NLCs progressively prevents the adhesion of biofilms to the body interior surfaces. In the future, these systems will be beneficial for creating fortified or functional food products by efficiently delivering bioactive compounds and nutrients.