Due to their size and difficulty to obtain cost/effective biological or synthetic receptors (e.g. antibodies or aptamers, respectively), organic toxic compounds (e.g. less than 1 kDa) are generally challenging to be detected using simple platforms such as biosensors. This study reports on the synthesis and characterization of a novel multifunctional composite material, magnetic silica beads/graphene quantum dots/molecularly imprinted polypyrrole (mSGP). mSGP is engineered to specifically and effectively capture and signal small molecules due to the synergy among chemical, magnetic and optical properties combined with molecular imprinting of tributyltin (291 Da), a hazardous compound, selected as a model analyte. Magnetic and selective properties of the mSGP composite can be exploited to capture and pre-concentrate the analyte onto its surface and its photoluminescent graphene quantum dots, which are quenched upon analyte recognition, are used to interrogate the presence of the contaminant. This multifunctional material enables a rapid, simple and sensitive platform for small molecule detection even in complex mediums such as seawater without any sample treatment.