The pericarp of purple corn has traditionally been thought of as being a byproduct. However, it is an excellent source of high-value polyphenols (such as anthocyanins, proanthocyanins, etc.) that could be extracted and used as nutraceuticals, cosmeceuticals, and valuable starting material for synthesizing food colorants and food additives. Hence, this study aimed to optimize the recovery of anthocyanins, phenolic acids, and condensed tannins (CT) from purple corn pericarp using a two-stage multivariate design and evaluated the phenolic profiles, antioxidants, product quality, and structural characteristics of the recovered extracts. According to Plackett-Burman design (PBD) screening, the key extraction variables identified were acetic acid concentration, extraction time, and ethanol concentration. This was followed by optimization using Box-Behnken design (BBD), facial central composite design (FCCD), and full-factorial design (FFD), and the best design was identified after comparative analysis. The models were found to be acceptable, as evidenced by the desirability values of 0.836–0.933. A comparison of the BBD, FCCD, and FFD was done, and it was found that the PBD-BBD produced a lower residual standard error (RSE) than the PBD-FCCD for most of the responses and yielded the lowest extraction time (∼8.6 h), proving that the BBD could forecast the data more accurately. To evaluate the extracts' bioactive extraction efficiency, antioxidant properties, product quality, and structural parameters, samples from a single factor (SF) experiment and BBD were compared. The BBD extract had better color properties (lower ΔE, higher a*, C, and H0) and a greater extraction yield (17.5%) than SF and was confirmed by the principal component and hierarchical cluster analysis. Although the scanning electron microscopy and the optical profilometer for BBD revealed irregular, loosely arranged granules, it had a less adverse effect on product quality and aligned with the Fourier transform infrared spectroscopy results. The BBD samples had lower levels of phenolic acids but higher levels of total phenolic content (118.86 ± 3.60 g GAE/kg), condensed tannins (231.74 ± 8.45 g EE/kg), antioxidants, cyanidin-3-glucoside (90.46 ± 4.47 mg/g), naringin (7.68 ± 0.58 mg/g), and cyanidin-chloride (49.81 ± 1.78 mg/g). This shows that BBD can effectively be used to optimize the extraction of polyphenolic compounds from purple corn pericarp using optimal extraction conditions, resulting in a higher yield of polyphenols having superior antioxidant properties and product quality in a comparatively shorter extraction time.