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Nanoplasmonic sensors based on surface-enhanced spectroscopies carry profound promise toward ultrasensitive detection of biomolecular analytes within miniaturized measurement footprints. High sensitivity in these sensors is achieved by intense electromagnetic (EM) enhancements at hot spots and colocalization of analytes with such hot spots. However, EM hot spots exhibiting high EM enhancements often present confined areas that render them inaccessible to large analytes such as biomolecules. Addressing this requires rational engineering of a nanoplasmonic interface that factors in the analyte surface concentrations and how they are distributed with respect to the EM hot spots. Here we demonstrate combination of metal-enhanced fluorescence (MEF) with a quartz crystal microbalance (QCM) through fabrication of highly resolved plasmonic nanoarrays directly on the QCM sensor. QCM and MEF are simultaneously employed to monitor in situ, real-time binding of fluorescently labeled protein to receptor-functionalized plasmonic arrays. The correlation between the QCM and MEF responses is used to quantify surface density of protein that contributes to the MEF signal intensities and obtain analyte distribution with respect to the EM hot spots by geometric modeling. Results further reveal the MEF assays to be sensitive down to ∼2 zmol of protein within measurement footprints that are 8 orders of magnitude smaller than that of the QCM.