Here we present the synthesis of site specific, protease (trypsin) cleavable, hydrophobic peptide polymer conjugate nanoparticles in inverse miniemulsion. Different peptide sequences were synthesized by microwave-assisted solid-phase synthesis and characterized by HPLC, NMR, and MALDI-TOF MS. The peptides were used to cross-link a hydrophobic functional polymer with standard peptide-coupling chemistry in inverse miniemulsion, thus generating the desired nanoparticulate morphology. By these means, well-defined nanoparticles in the size range of 200-300 nm were obtained. After transferring the particles into aqueous medium, they were characterized with photon cross-correlation spectroscopy (PCCS) and scanning electron microscopy (SEM). After removal of the solvent, the degree of cross-linking was determined by (15)N solid-state NMR. Integration of a fluorophore/quencher system, based on fluorescence resonance energy transfer (FRET) in the peptide sequences, enabled the monitoring of site specific recognition of cross-linked polymeric nanostructures by enzymes, resulting in a fluorescence recovery upon cleavage of the peptide.