Due to threat coming from viral diseases, mainly from influenza, new assays and devices are investigated. This study is aimed at developing of low-cost isolation and detection of specific influenza protein hemagglutinin (HA) labelled with CdS, PbS, and CuS quantum dots. The influenza protein was determined via concentration of cadmium(II), lead(II), and copper(II) ions contained in quantum dots using stopped flow injection analysis with electrochemical detection (SFIA-ED). The main attention was devoted to detection of quantum dots and optimization of the whole analytical system. A particular aim was focused on an application of streptavidin-coated paramagnetic particles that were modified with biotinylated glycan. In addition, their selective binding properties to the influenza virus were monitored. Based on the results it can be concluded that CdS QDs were the best label for viral protein determination.