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Over the past two decades, higher efficiencies have become the goal of most research organizations, and more so for high throughput synthesis. Consequently, there is an urgent need for an advanced purification approach to accommodate the large number of small molecules in a shorter turnaround time. To address this, an efficient and high throughput purification method was developed leveraging the superficially porous particle (SPP) column technology, which was optimized with respect to detector acquisition rate, flow rate, and gradient time. The experiments were performed using a sample mixture of six commercially available small molecules including Nicotinamide (NIC), 4-Amino benzophenone (ABP), Praziquantel (PRA), butyl‑4-hydroxybenzoate (BHB), Warfarin sodium (WAR), and Ibuprofen (IBU). The study outcomes were promising and exhibited a good separation of all six analytes with ∼83 % less turnaround time and ∼65 % less solvent consumption than the regular methods. Furthermore, it showed significant improvement in peak symmetry, capacity factor, and resolution for all six analytes and afforded superior chromatographic performance than the regular method with fully porous particle (FPP) columns. The study concludes that SPP columns provide cost-effective, eco-friendly, and high throughput purification of small molecules.