In this study, malachite green-imprinted sol-gel polymer (MG-imp) has been anchored on the surface of mercaptopropyltrimethoxysilane-capped Mn-doped ZnS quantum dots (MPTMS-Mn:ZnS) and characterised by Fourier Transform-Infrared Spectroscopy and Scanning Electron Microscopy. Surface imprinting property of MPTMS-Mn:ZnS (QDs) covered by MG-imprinted sol-gel (MG-imp-QDs) was elucidated by differential pulse voltammetry and room temperature phosphorescence (RTP) measurements. Selective determination of MG in the presence of analogue molecules was managed upon optimised solution parameters based on the RPT quenching efficiency of MG-imp-QDs nanoparticles. Electrochemical measurement was also carried out by fabricating electrode modified with MG-imp-QDs nanoparticles in order to confirm the existence of imprinting effect and spectral overlap causing to inner filter effect during the RTP measurements. The linear concentration range and limit of detection for determining of MG in buffer solution were found to be 0.03-1.84 mu M and 3.2 nM, respectively.