Chemical weathering of archaeological material is well known; however, while there have been a number of experimental studies demonstrating different types and degrees of chemical alteration on faunal remains, little attention has been paid to stone tools, and the few studies that exist relate mainly to siliceous materials and water-induced chemical alteration. Azokh Cave, located in the South Caucasus, contains a Middle Pleistocene to Holocene infill, and detailed macro- and microscopic examination of the lithic assemblages recovered there indicates potential chemical weathering of the stone artefacts. The cave is also currently home to one of the largest bat colonies in the region, and their guano forms a significant component of the infill of the inner galleries. Based on these two factors, an experimental pilot study was set up to artificially chemically alter a range of stone flakes produced specifically for the task, in order to determine the nature and likely cause of weathering. The experimental flakes, produced from different raw materials, were buried in fresh bat guano for up to two years. The results reported herein demonstrate that in a relatively short time, the highly acidic composition of bat guano strongly affects calcium-bearing rocks (e.g., limestone, basalt) altering their entire surface. Similar comparisons may be made with chemical alteration evident on archaeological lithics from Azokh Cave, suggesting that bat guano has played a significant role in diagenetic alteration.