Objectives <p>To investigate the impact of three commonly used cleaning methods—mechanical cleaning, chemical cleaning, and ultrasonic cleaning—on the optical transmittance and surface roughness of thermoplastic orthodontic retainers following coffee-induced staining.</p> Materials and methods <p>Standardized thermoplastic specimens were assigned to five groups (<i>n</i> = 10): an unstained control group, a coffee-stained group without cleaning, and three post-staining cleaning groups treated with either mechanical cleaning, chemical cleaning using Polident tablets, or ultrasonic cleaning. Optical transmittance was measured using ultraviolet–visible (UV–Vis) spectrophotometry. Surface roughness parameters (Ra, Rz, RSm) were analyzed via surface profilometer, and surface morphology was examined using scanning electron microscopy (SEM).</p> Results <p>Coffee staining significantly reduced transmittance and increased surface roughness, indicating adverse effects on both optical transmittance and microstructural integrity. Ultrasonic cleaning effectively restored transmittance and surface integrity to near-control levels, with minimal surface damage. Mechanical cleaning successfully removed surface stains but introduced linear abrasions and led to a significant decrease in RSm values. Chemical cleaning achieved moderate stain removal but left visible surface residues.</p> Conclusions <p>Among the cleaning protocols evaluated, ultrasonic cleaning demonstrated superior performance in stain removal and preservation of surface integrity. Mechanical cleaning was effective but caused surface wear, while chemical cleaning offered limited cleaning efficacy and left undesirable deposits.</p> Clinical relevance <p>Cleaning strategies for orthodontic retainers should balance stain removal efficiency with material preservation. Ultrasonic cleaning provides a clinically favorable option, offering effective cleaning with minimal adverse effects on surface characteristics.</p>