Microfabrication technologies have extensively advanced over the past decades, realizing a variety of well-designed compact devices for material synthesis, separation, analysis, monitoring, sensing, and so on. The performance of such devices has been undoubtedly improved, while it is still challenging to build up a platform by rationally combining multiple processes toward practical demands which become more diverse and complicated. Here, we present a simple and effective microfluidic system to produce and immobilize a well-defined functional material for on-chip permanganate (MnO4−) sensing. A droplet-based microfluidic approach that can continuously produce monodispersed droplets in a water-in-oil system is employed to prepare highly uniform microspheres (average size: 102 μm, coefficient of variation: 3.7%) composed of bovine serum albumin (BSA) hydrogel with autofluorescence properties in the presence of glutaraldehyde (GA). Each BSA hydrogel microsphere is subsequently immobilized in a microchannel with a hydrodynamic trapping structure to serve as an independent fluorescence unit. Various anions such as Cl−, NO3−, PO43−, Br−, BrO3−, ClO4−, SCN−, HCO3−, and MnO4− are individually flowed into the microchannel, resulting in significant fluorescence quenching only in the case of MnO4−. Linear correlation is confirmed at an MnO4− concentration from 20 to 80 μM, and a limit of detection is estimated to be 1.7 μM. Furthermore, we demonstrate the simultaneous immobilization of two kinds of different microspheres in parallel microchannels, pure BSA hydrogel microspheres and BSA hydrogel microspheres containing rhodamine B molecules, making it possible to acquire two fluorescence signals (green and yellow). The present microfluidics-based combined approach will be useful to record a fingerprint of complicated samples for sensing/identification purposes by flexibly designing the size and composition of the BSA hydrogel microspheres, immobilizing them in a desired manner and obtaining a specific pattern.