We report on a novel strategy to tune the structural and optical properties of luminescent alloyed quantum dot (QD) nanocrystals using plasmonic gold (Au) and silver (Ag) nanoparticles (NPs). Alloyed CdZnSeS QDs were synthesized via the organometallic synthetic route with different fabrication strategies that involve alternative utilization of blends of organic surfactants, ligands, capping agents, and plasmonic oleylamine (OLA)-functionalized AuNPs and AgNPs. Ligand exchange with thiol l-cysteine (l-cyst) was used to prepare the hydrophilic nanocrystals. Analysis of the structural properties using powder X-ray diffraction revealed that under the same experimental condition, the plasmonic NPs altered the diffractive crystal structure of the alloyed QDs. Depending on the fabrication strategy, the crystal nature of OLA-AuNP-assisted CdZnSeS QDs was a pure hexagonal wurtzite domain and a cubic zinc-blende domain, whereas the diffraction pattern of OLA-AgNP-assisted CdZnSeS QDs was dominantly a cubic zinc-blende domain. Insights into the growth morphology of the QDs revealed a steady transformation from a heterogeneous growth pattern to a homogenous growth pattern that was strongly influenced by the plasmonic NPs. Tuning the optical properties of the alloyed QDs via plasmonic optical engineering showed that the photoluminescence (PL) quantum yield (QY) of the AuNP-assisted l-cyst-CdZnSeS QDs was tuned from 10 to 31%, whereas the PL QY of the AgNP-assisted l-cyst-CdZnSeS QDs was tuned from 15 to 90%. The low PL QY was associated with the surface defect state, while the remarkably high PL QY exhibited by the AgNP-assisted l-cyst-CdZnSeS QDs lends strong affirmation that the fabrication strategy employed in this work provides a unique opportunity to create single ensemble, multifunctional, highly fluorescent alloyed QDs for tailored biological applications.