Biofunctionalized quantum dots (QDs) are effective target fluorescent labels for bioimaging. However, conventional synthesis of biofunctionalized I-III-VI core-shell CuInS2/ZnS QDs requires complex bench-top operations, resulting in limited product performance and variety, and is not amenable to a 'one-step' approach. In this work, we have successfully demonstrated a fully automated method for preparing denatured bovine serum albumin (dBSA)-CuInS2/ZnS QDs by introducing microfluidic (MF) chips to synthesize biofunctionalized QDs, hence establishing a 'one-step' procedure. We have also studied and optimized the reaction synthesis parameters. The emission wavelength of the dBSA-CuInS2/ZnS QDs is located in the near-infrared range and can be tuned from 650 to 750 nm by simply varying the reaction parameters. In addition, the 'one-step'-synthesized dBSA-CuInS2/ZnS QDs have a long average fluorescence lifetime of 153.76 ns and a small particle size of 5 ± 2 nm. To demonstrate the applicability of the 'one-step'-synthesized dBSA-CuInS2/ZnS QDs in bioimaging studies, we modified the QDs with folic acid and hyaluronic acid, and then performed target bioimaging and cytotoxicity tests on macrophages, liver cancer cells and pancreatic cancer cells. The cell images show that the red emission signals originate from the QDs, which indicates that the dBSA-CuInS2/ZnS QDs prepared by the MF approach are suitable optical contrast agents for target bioimaging. This 'one-step' MF-based QD synthesis approach could serve as a rapid, cost-effective, and small-scale nanocrystal production platform for complex QD formulations for a wide range of bioapplications.