Cellular interactions with engineered nanoparticles (NPs) are dependent on many properties, inherent to the nanoparticle (viz. size, shape, surface characteristics, degradation, agglomeration/dispersal, and charge, etc.). Modification of the surface reactivity via surface functionalization of the nanoparticles to be targeted seems to be important. Utilization of different surface functionalization methods of nanoparticles is an emerging field of basic and applied nanotechnology. It is well known that many disease-causing organisms induce host lipids and if deprived, their growth is inhibited in vivo. Amorphous nanosilica (ANS) and amorphous microsilica with nanopores (AMS) were prepared by a combination of wet chemistry and high-energy ball milling. Lipophilic moieties were attached to both ANS and AMS via chemical surface functionalization method. Lipophilic ANS and AMS were found to inhibit the growth of Bombyx mori nuclear polyhedrosis virus (BmNPV) and chicken malarial parasites via absorption of silkworm hemolymph and chicken serum lipids/lipoproteins, respectively, in vivo. Therefore, intelligent surface functionalization of NP is an important concept, and its application in curing chicken malaria and BmNPV is presented here. Surface functionalization method reported in this paper might serve as a valuable technology for treating many diseases where pathogens induce host lipid.