Systems and methods are provided herein for the extraction, detection and measurement of MNPs in complex matrices in particular, the method includes mixing a solution including a predetermined organic substance with a matrix including the metal nanoparticles, the predetermined organic substance adapted to bind to the metal nanoparticles, to facilitate extraction by an organic solvent and to provide a distinct SERS signal, the mixing resulting in a suspension, adding a solution of a predetermined organic extraction solvent to the suspension, extracting and separating the metal nanoparticles; the metal nanoparticles, after extraction, functionalized by binding with the predetermined organic substance, and extracting and separating the metal nanoparticles; the metal nanoparticles, after extraction, functionalized by binding with the predetermined organic substance; and performing SERS imaging on the functionalized metal nanoparticles in order to detect metals nanoparticles.