The hyperarid core of the Atacama Desert is one of the driest and most inhospitable places on Earth, where life is most commonly found in the interior of rocks (i.e., endolithic habitats). Due to the extreme dryness, microbial activity in these habitats is expected to be low; however, the rate of carbon cycling within these microbial communities remains unknown. We address this issue by characterizing the isotopic composition ((13)C and (14)C) of phospholipid fatty acids (PLFA) and glycolipid fatty acids (GLFA) in colonized rocks from four different sites inside the hyperarid core. δ(13)C results suggest that autotrophy and/or quantitative conversion of organic matter to CO2 are the dominant processes occurring with the rock. Most Δ(14)C signatures of PLFA and GLFA were consistent with modern atmospheric CO2, indicating that endoliths are using atmospheric carbon as a primary carbon source and are also cycling carbon quickly. However, at one site the PLFA contained (14)C from atmospheric nuclear weapons testing that occurred during the 1950s and 1960s, indicating a decadal rate of carbon cycling. At the driest site (Yungay), based on the relative abundance and (14)C content of GLFA and PLFA, there was evidence of possible preservation. Hence, in low-moisture conditions, glycolipids may persist while phospholipids are preferentially hydrolyzed.