In this report, we address an important issue associated with the utilization of excellent plasmonic properties of shape-anisotropic gold nanostructures for sensing application. Plasmonic nanoparticles having shapes of rods, triangles, cubes, stars, etc. are typically synthesized using surfactant assisted approaches. The utilized surfactants such as cetyltrimethylammonium bromide/chloride (CTAB/C) are afterwards still present on its surface and compromise the film formation ability on substrates such as glass surfaces. In this regard, we report a two step process for the ligand exchange as a combination of extraction and exchange reaction using poly(sodium 4-styrenesulfonate) (PSS) and trisodium citrate (TSC). CTAC stabilized gold nano cubes (CTAC/Au-NCs) synthesized using a microfluidic synthesis procedure were successfully deposited on silane modified glass substrate after ligand exchange from CTAC/Au-NCs to TSC stabilized gold nano cubes (TSC/Au-NCs). Further, TSC/Au-NCs were found to be highly stable and suitable for microfluidic sensing of different glucose concentrations using localized surface plasmon resonance (LSPR) spectroscopy offering a highly improved sensitivity (126.37 nm/RIU). The proposed method is also a promising tool for the immobilization of (CTAC/Au-NCs) protected other gold nanostructures such as rods, trangles, prism etc. on glass slide for optical sensing applications.