Fluorescence from quantum dots (QDs) sandwiched between colloidal gold nanoparticles and lithographically created metal nanoarrays is studied using engineered peptides as binding agents. For optimized structures, a 15-fold increase is observed in the brightness of the QDs due to plasmon-enhanced fluorescence. This enhanced brightness is achieved by systematically tuning the vertical distance of the QD from the gold nanoparticles using solid-specific peptide linkers and by optimizing the localized surface plasmon resonance by varying the geometric arrangement of the patterned gold nanoarray. The size and pitch of the patterned array affect the observed enhancement, and sandwiching the QDs between the patterned features and colloidal gold nanoparticles yields even larger enhancements due to the increase in local electromagnetic hot spots induced by the increased surface roughness. The use of bifunctional biomolecular linkers to control the formation of hot spots in sandwich structures provides new ways to fabricate hybrid nanomaterials of architecturally induced functionality for biotechnology and photonics.