Metal nanoparticles, especially when synthesized on a large scale, often exhibit significant heterogeneity in size and shape, which can limit their reliability and reproducibility in various applications, including plasmonics. This study introduces a centrifugal depletion-induced flocculation (CDF) method for the scalable and efficient purification of Au nanocubes (AuNCs). Unlike traditional flocculation methods, CDF leverages controlled centrifugation and depletion interactions to achieve high particle homogeneity and recovery efficiency while significantly reducing processing time. Systematic optimization of critical parameters, such as nanoparticle concentration, centrifugal force, and flocculation time, enabled recovery efficiency exceeding 98% and yields of approximately 98–99% for 60 nm AuNCs. The adaptability of this method was also demonstrated for NCs of varying sizes and larger volumes, underscoring its versatility and scalability for diverse nanoparticle systems. The superior monodispersity and shape uniformity of purified AuNCs achieved through this approach hold significant potential for applications requiring precise control over plasmonic properties, such as high-performance optical sensors and integrated nanophotonic systems.