Synthesis, characterization and bifunctional applications of silver nanoparticles with two different surface capping reagents are reported. The surface engineering of AgNPs with 1-octadecanethiol (1-ODT)/4-aminothiophenol (4-AMP) ‘Ag@ODT/AMP’ and 1-octadecanethiol (1-ODT)/1-thioglycerol (1-TG) ‘Ag@ODT/TG’ were synthesized, characterized and applied for microextraction. The presence of two functional groups on the surface of AgNPs produced a multidendate that can interact with proteins and peptides such as insulin, heart cytochrome c, ubiquitin, lysozyme, cysteine, and homocysteine. Thus, they were applied in a single drop microextraction (SDME) process termed as silver nanoparticle assisted single drop microextraction (SASDME). The proteins after separation were analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The effects of different parameters were optimized, such as sample pH, stirring rate, salt concentration, extraction time, matrix type, and the amount of AgNPs. The present methodology has been successfully applied for the detection of insulin and cytochrome c in real samples (urine and milk) and for cysteine and homocysteine in a urine sample. SASDME is a simple and effective microextraction technique for real sample analysis, which is rapid and possesses high sensitivity and selectivity.