The objective of this study was to develop and validate a near-infrared (NIR) spectroscopy based method for in-line quantification during the second alcohol precipitation process of Astragali radix. In total, 22 calibration experiments were carefully arranged using a Box–Behnken design. Variations in the raw materials, critical process parameters, and environmental temperature were all included in the experimental design. Two independent validation sets were built for method evaluation. Validation set 1 was used for optimization. Different spectral pretreatments were compared using a “trial-and-error” approach. To reduce the calculation times, the full-factorial design was applied to determine the potential optimal combinations. Then, the best parameters for the pretreatment algorithms were compared and selected. Partial least squares (PLS) regression models were obtained with low complexity and good predictive performance. Validation set 2 was used for a thorough validation of the NIR spectroscopy method. Based on the same validation set, traditional chemometric validation and validation using accuracy profiles were conducted and compared. Conventional chemometric parameters were used to obtain the overall predictive capability of the established models; however, these parameters were insufficient for pharmaceutical regulatory requirements. Then, the method was fully validated according to the ICH Q2(R1) guideline and using the accuracy profile approach, which enabled visual and reliable representation of the future performances of the analytical method. The developed method was able to determine content ranges of 8.44–39.8% at 0.541–2.26 mg/mL, 0.118–0.502 mg/mL, 0.220–0.940 mg/mL, 0.106–0.167 mg/mL, 0.484–0.879 mg/mL, and 0.137–0.320 mg/mL for total solid, calycosin glucoside, formononetin glucoside, 9, 10-dimethoxypterocarpan glucopyranoside, 2′-dihydroxy -3′, 4′-dimethoxyisoflavan glucopyranoside, astragloside II, and astragloside IV, respectively. These ranges were specific to the early and middle stages of the second alcohol precipitation process. The method was confirmed to be capable of achieving an in-line prediction with a very acceptable accuracy. The present study demonstrates that accuracy profiles offer a potential approach for the standardization of NIR spectroscopy method validation for traditional Chinese medicines (TCMs).