Herein, we report the formation of a crystalline assembly of gold (Au) nanoclusters for cancer theranostics via active targeting of mitochondria. To the best of our knowledge, this is the first report of the target specific activity of an “assembly of gold nanoclusters”. Au14 nanoclusters were stabilized with mercaptopropionic acid and L-tyrosine. The limited solubility of L-tyrosine in methanolic solution led to the formation of a polycrystalline assembly of Au nanoclusters via interactions between ligands (tyrosine) stabilizing the clusters. Further, complexation reaction between zinc ions and ligands stabilizing the Au nanoclusters led to the formation of a single crystalline assembly of gold nanoclusters. Transmission electron microscopic and selected area electron diffraction analyses revealed the formation of faceted crystals with a hexagonal arrangement of Au14 nanoclusters. A theoretical structure of the crystalline complex of Au nanoclusters and zinc ions has been proposed herein based on experimental observations and computational optimization. The crystalline assembly of Au nanoclusters, formed via ligand association as well as complexation reaction, exhibited mitochondria targeted anti-cancer activity – as verified by Mito Tracker staining experiments. However, the MTT assay, FACS analysis and JC-1 staining experiments revealed that the zinc mediated assembly of Au nanoclusters exhibited superior therapeutic action as compared to the methanol driven assembly of the clusters.