Semiconductor nanocrystal quantum dots find several applications in nanotechnology. Particularly in device applications, such quantum dots are typically required to be assembled with specific distribution in space for enhanced functionality and placed at desired spatial locations on the device which commonly has several diverse material components. In conventional approaches, self-assembly of nanocrystals typically takes place nonspecifically without surface recognition of materials and cannot meet these requirements. To remedy these issues, we proposed and demonstrated uniform, controlled, and targeted self-assembly of quantum dot emitters on multi-material devices by using cross-specificity of genetically engineered peptides as smart linkers and achieved directed immobilization of these quantum dot emitters decorated with peptides only on the targeted specific regions of our color-conversion LEDs. Our peptide decorated quantum dots exhibited 270 times stronger photoluminescence intensity compared to their negative control groups.