Small mammals are a key study element for paleoenvironmental and paleoclimatic reconstruction, especially in the case of rodents due to their high adaptability. Their teeth play a crucial role in these studies for taxonomic assignment and the identification of taphonomic accumulation agents. Small rodent teeth, due to their size, are typically cleaned using chemical methods; however, this approach lacks precision and can harm materials. This study aimed to evaluate different cleaning methods on a sample of Meriones teeth with carbonate concretions from Kaldar Cave (Iran), not only to evaluate their efficacy, but also to characterise the possible modifications. The surface and composition of the samples were documented through microcomputed tomography and analysed before and after cleaning to identify any changes. Three cleaning reagents were tested based on sedimentary matrix and tooth composition: acetic acid, Tetrasodium ethylenediaminetetraacetic acid (EDTA), and sodium hexametaphosphate. These products were applied individually, in combination with mechanical cleaning and ultrasounds bath. Acetic acid and EDTA were the most successful in removing concretions, whereas sodium hexametaphosphate was less effective. However, the study revealed that these cleaning methods could cause some surface modifications, including scratches, volumetric losses, dentine displacement, opacity, and changes resembling digestion processes. These alterations must be considered when applying these methods to avoid interference with subsequent taphonomic or taxonomic studies.