Plasmon-enhanced fluorescence (PEF)-based analytical technology has recently demonstrated its ability in detecting biomarkers with ultrahigh sensitivity. However, the scope of the PEF-based technology has been hindered by its reliance on flat substrates with relatively low binding kinetics and the limited multiplex detection ability. Herein, we reported a simple yet robust method for the fabrication of plasmonic magnetic microbeads (PMMBs)-based suspension array technology (SAT) with fluorescence enhancement of about 60-fold, improving the detection limit of biomarkers by 2-orders of magnitude toward 100 fM. We also demonstrated the performance of this method for the detection of anti-acidic ribosomal phosphoprotein 0 (anti-P0) autoantibody in sera from systemic lupus erythematosus (SLE) patients. Owing to the high sensitivity and efficient magnet-based sample collection, our method can be employed for detection of ultrasmall volumes of samples (e.g., 2 μL), promising for point-of-care detection. Furthermore, a size-encoded PMMBs-based multiplexed suspension array for simultaneous detection of multiple biomarkers is realized, illustrating the great potential of this technology in high-throughput disease diagnosis applications.