Stable and highly emissive gold nanoclusters were successfully synthesized by means of stabilization with PIPES (PIPES-Au NCs, where PIPES = 1,4-piperazinediethanesulfonic acid) using a thermal synthetic strategy. By varying the amount of PIPES, two Au NCs with different emission maxima were obtained. The synthesized Au NCs were successfully incorporated into a porous silica matrix to generate fluorescent PIPES-Au NC doped silica nanoparticles. Sequential doping of the PIPES-Au NCs with tetraethylorthosilicate (TEOS) and 3-(aminopropyl)triethoxysilane (APTS) furnished a silica matrix, which effectively protected the PIPES-Au NCs during repeated washing with polar solvent and the composite of which exhibited enhanced emission.