This study describes an innovative in-line near-infrared (NIR) process monitoring method for the quantification of the total polyphenolic content (TPC) of Ajuga genevensis dry extracts. The dry extract was obtained in a fluidized bed processor, by spraying and adsorbing a liquid extract onto an inert powder support. NIR spectra were recorded continuously during the extract’s spraying process. For the calibration of the in-line TPC quantification method, samples were collected during the entire process. The TPC of each sample was assessed spectroscopically, by applying a UV-Vis reference method. The obtained values were further used in order to develop a quality OPLS prediction model by correlating them with the corresponding NIR spectra. The final dry extract registered good flowability and compressibility properties, a concentration in active principles three times higher than the one of the liquid extract and an overall process yield of 85%. The average TPC’s recovery of the NIR in-line prediction method, compared with the reference UV-Vis one, was 98.7%, indicating a reliable monitoring method which provided accurate predictions of the TPC during the process, permitting a good process overview and enabling us to establish the process’s end point at the exact moment when the product reaches the desired TPC concentration.