The removal of analog impurities with a very small sample size presents a major challenge in the purification of high-valued biochemicals such as those derived from fermentation or herbs. Ganoderic acid T (GA-T), an antitumor drug candidate, is very difficult to purify from the mycelia of medicinal mushroom Ganoderma lucidum due to co-purifying analog impurities. A novel pretreatment process with three consecutive chemical conversion steps, namely hydrolysis-acetylation-hydrolysis, was developed to convert two key analog impurities (7-O-ethyl GA-O and GA-Mk) to GA-T. It increased the GA-T amount in the 100 g dried mycelia from the initial 0.444 g to 1.621 g after the pretreatment, representing an apparent yield of 365% for the pretreatment. If the yield basis were the initial GA-T amount plus the GA-T amount from 100% conversion of 7-O-ethyl GA-O and GA-Mk in the crude extract, the yield, termed adjusted yield for the pretreatment in this work, would still reach 90.8%. Furthermore, the subsequent RP-HPLC purification was considerably enhanced due to the conversion of the analog impurities. This game-changer strategy achieved a daily GA-T throughput of 2.9 g with 95% purity (mass based). Even at the laboratory scale, it is now possible to produce a sufficient amount of GA-T for small-scale pharmacological and clinical evaluations. The approach of converting analog impurities that are otherwise difficult to remove to the product in a bioseparation process may be useful to achieve enhanced recovery of other medicinally useful natural products.