Electrochemical detection of cadmium-selenide/zinc-sulfide (CdSe@ZnS) quantum dots (QDs) as labeling carriers in an assay for apolipoprotein E (ApoE) detection has been evaluated. The immunocomplex was performed by using tosylactivated magnetic beads as preconcentration platform into a flexible hybrid polydimethylsiloxane (PDMS)-polycarbonate (PC) microfluidic chip with integrated screen printed electrodes (SPE). All the immunoassay was performed in chip and in flow mode. The sensitive electrochemical detection was obtained by square wave anodic stripping voltammetry. ApoE was evaluated for its potential as biomarker for Alzheimer’s disease detection, achieving a limit of detection (LOD) of ∼12.5 ng mL−1 with a linear range from 10 to 200 ng mL−1 and high accuracy for diluted human plasma.