Translation of a manual process to high throughput for research and development requires special consideration. One important and often unreported aspect is the establishment of an efficient cleaning routine. This becomes significant, as precious time and, in particular, material would be lost, that is, when low-quality high-throughput experimentation is involved. We present a fully automated cleaning routine of the challenging synthesis of cadmium selenide quantum dots. Manual, semiautomated, and fully automated cleaning protocols were executed and compared in terms of spectral similarities of the synthesized colloids. Only the fully automated protocol enabled true 24/7 operation.