Polymerase Chain Reaction (PCR)-based assays were widely deployed during the SARS-CoV-2 pandemic for population-scale testing. High-throughput molecular diagnostic labora-tories required a high degree of process automation to cope with huge testing demand, fast turn-around times and quality requirements. However, the critical step of preparing a PCR MasterMix has often been neglected by process developers and optimisers, and is largely dependent upon operator skill for the manual pipetting of reagents to construct the PCR MasterMix. Dependence on manual procedures introduces variation, inconsistency, wastage and potentially risks data integrity. To address this issue, we developed a liquid-handler based solution for automated, traceable and compliant PCR MasterMix preparation. Here, we show that a fully automated PCR MasterMix protocol can substitute manual pipetting, without affecting clinical calling, accuracy or precision. Ultimately, this method reduced cost-per-test at a high-throughput laboratory by eliminating operator-induced wastage while improving the quality of results.