This research aims to optimize the silk and wool dyeing process using natural dyes from Bixa orellana (annatto) through response surface methodology. Central composite design experiments highlight the significant enhancement of color outcomes achieved through microwave treatment. For silk, the optimal conditions (80 °C for 40 min) with annatto extract yield a color strength (K/S) of 17.8588, while wool achieves a K/S of 7.5329. Introducing eco-friendly bio-mordants, such as pomegranate peel and red sumac tannins, enhances color strength. Pre-dyeing treatments with 2% red sumac, 1.5% pomegranate peel, and weld flower extracts for silk produce high color strength, with K/S values of 16.4063, 16.3784, and 12.1658, respectively. Post-dyeing, the K/S values increase to 40.1178, 17.4779, and 21.6494. Wool yarn exhibits similar improvements, with pre-dyeing K/S values of 13.1353, 13.5060, and 16.3232, escalating to 10.5892, 15.3141, and 23.4850 post-dyeing. Furthermore, this research underscores improved colorfastness properties, including notable enhancements in light, wash, and rubbing fastness for both silk fabric and wool yarn. These findings underscore the efficacy of the proposed sustainable dyeing methods, offering valuable insights for eco-friendly textile production.