In this study, we constructed a system for on-the-fly NP detection in a minute sample (down to 5 µL) that combined sample mixing and NP quantification in a single step. The system utilized a fluid-control technique based on vibration-induced flow (VIF) in which localized flow was induced around the micropillars by applying small periodic vibrations to the entire substrate. Previously, VIF (including acoustic streaming flow) was applied to enhance micromixing. In this study, we examined the method by which VIF-induced local mixing of a fluid containing target NPs and affinity capture beads enhanced the aggregation of affinity microbeads. First, the behavior of the VIF on capture-bead aggregation was characterized using model NPs and affinity capture beads. Next, we showed that the time evolution of the size of the aggregates could be related to the concentration of NPs in the sample, verifying that this system can be used for the quantitative evaluation of NPs. Finally, we demonstrated that the exosome concentration can be evaluated using T-cell immunoglobulin and mucin domain-containing protein 4 (Tim-4)-conjugated magnetic capture beads to validate the usefulness of the system for real diagnostic applications.