The significant rise in the use of clear aligners for orthodontic treatment is attributed to their aesthetic appeal, enhancing patient appearance and self-confidence. The aim of this study is to evaluate the aligners’ response to common staining agents (coffee, black tea, Coca-Cola, and Red Bull) in color and chemical stability. Polyurethane-based thermoformed and 3D-printed aligners from four brands were exposed to common beverages to assess color change using a VITA Easyshade compact colorimeter after 24 h, 48 h, 72 h, and 7 days, as well as chemical stability using ATR-FTIR spectroscopy. The brand, beverage, and manufacturing method significantly influence color stability. ATR-FTIR analysis revealed compositional differences, with variations in response to beverage exposure affecting the integrity of polymer bonds. Color change analysis showed coffee as the most potent staining agent, particularly affecting Tera Harz TC85 aligners, while ClearCorrect aligners exhibited the least susceptibility. 3D-printed aligners showed a greater color change compared to thermoformed ones. Aligners with a PETG outer layer are more resistant to stains and chemical alterations than those made of polyurethane. Additionally, 3D-printed polyurethane aligners stain more than thermoformed ones. Therefore, PETG-layered aligners are a more reliable choice for maintaining the aesthetic integrity of aligners.