Advancement in chemistry holds a great promise in improving drug encapsulation that leads to superior drug delivery efficiency and the therapeutic efficacy of nano/micro-delivery systems. Drugs are being designed to specifically access the infection sites via covalent conjugation to nano/micro-delivery systems. This chapter focuses on techniques for achieving covalent encapsulation of drugs in nano/micro-delivery systems, how conjugation is applied to selectively influence pharmacokinetic profile, intracellular, and extracellular uptake, specific targeting to disease sites, binding to specific receptors, and controlled/sustained release. In addition, the effect of conjugation on drug efficacy and biosafety of the micro/ nanoparticulate drug delivery systems are discussed.