BackgroundScientifically, isoflavones from Pueraria thomsonii Benth possess diverse pharmacological activities and have been used to treat various diseases. In vitro propagation of callus has contributed to the reliability for large-scale production of target compounds. However, the factors affecting the biosynthesis of major isoflavones daidzin, puerarin and daidzein in the callus culture of P. thomsonii are still not known. Therefore, we aimed to enhance the in vitro production of daidzin, puerarin and daidzein by optimizing three independent factors such as temperature, NAA and 6-BA concentrations.ResultsOur findings showed that the optimal concentrations for in vitro biomass production and efficient synthesis of puerarin, daidzin and daidzein were found to be 0.158%, 0.463% and 0.057%, respectively. In addition, the HPLC fingerprint with chemo-metrics analysis was constructed by linear regression of the puerarin, daidzin and daidzein which was found to be in the range of 1.0–36.0, 5.0–72.0 and 1.0–15.0 mg/mL and the LODs and LOQs were found to be 0.15, 0.52, 0.35 and 0.28, 1.50, 0.50 mg/mL for puerarin, daidzin and daidzein, respectively. Surprisingly, our results were also in agreement with the concentration obtained from the model verification for optimal and efficient production of puerarin, daidzin and daidzein which was found to be 0.162%, 0.458% and 0.049%, respectively.ConclusionsIn summary, our present investigation provides new insights that could facilitate the enhanced production of valuable isoflavones in P. thomsonii using plant cell cultures treated with appropriate elicitor combinations and temperature. As far as the authors are concerned, this is the first report on production of daidzin, puerarin and daidzein at higher yield at laboratory level for a wide range of applications in future food, medicinal and pharmaceutical companies.