Rapid, sensitive, and accurate detection of analytes present in low concentrations in complex matrixes is a critical challenge. One issue that affects many biosensor protocols is the number and nature of the interferences present in complex matrixes such as plasma, urine, stool, and environmental samples, resulting in loss of sensitivity and specificity. We have developed a method for rapid purification, concentration, and detection of target analytes from complex matrixes using antibody-coated superparamagnetic nanobeads (immunomagnetic beads, or IMBs). The surface plasmon resonance (SPR) detection signal from staphylococcal enterotoxin B (SEB) was dramatically increased when the IMBs were used as detection amplifiers. When SEB detection included a 10-fold concentration/purification IMB protocol, a substantial increase in detection sensitivity was observed. This procedure was used to successfully purify and concentrate SEB from serum and stool samples, then amplify the SPR detection signal. SEB at a concentration of 100 pg/mL was easily detected in both buffer and stool samples using this procedure. The IMB protocol also served to verify the analyte detection by using two different anti-SEB antibodies, mouse monoclonal antibodies attached to the magnetic nanobeads and rabbit polyclonal antibodies on the SPR sensor surface. Multiple detections of SEB in stool were performed using the same sensor surface by regenerating the sensor surfaces with a pH 2.2 buffer wash.