Thermoplastic materials are sensitive to humidity, temperature variations, enzyme activities, and cyclic loading. All these factors can cause changes to the mechanical properties of the material. The aim of this study was to determine the influence of different cleaning protocols on the surface roughness of orthodontic retainers. Samples of two brands of polyethylene terephthalate glycol (PET-G) material were exposed to four cleaning protocols: Corega (alkaline peroxide tablets), Toothbrush, Corega + toothbrush, Toothbrush + toothpaste, and Control. Measurement of the surface roughness of the sample on both the top and bottom side was carried out before and after cleaning. There was no statistical difference between the final values of the measured parameters. However, looking at the extent of the change in surface roughness, there was a statistically significant difference in the upper side of the Corega + toothbrush group between Materials A and B. This suggests that there was a greater change in the roughness of material A (Erkodur), given that the mean change in roughness of Material A was Ra 0.047, whereas the mean change in roughness of Material B was Ra 0.022. Almost all the tested cleaning procedures significantly increased the surface roughness of the PET-G retainer material. Of all the methods, the Corega tablets had the lowest influence on surface roughness.