The contribution of microbial residues to soil organic carbon (SOC) is a process highly influenced by soil properties. We evaluated the presence of microbial amino sugar residues in soil (0-50 cm) of control and warmed plots in an alpine meadow on the Qinghai-Tibet Plateau. Alpine grasslands in the Qinghai-Tibet Plateau store large amounts of soil C and are highly vulnerable to climate change. Results showed that warming significantly increased total microbial residues across the 0-50 cm soil depth. The proportion of microbial-derived C to SOC significantly increased in warmed plots (52% on average) by soil depth compared to the control (38%). Higher microbial turnover and selective preservation into organo-mineral complexes likely explains the observed result. Given insignificant change in total SOC, our results infer an alteration of the SOC source configuration (microbial-derived vs. plant-derived). The observed greater magnitude of warming effects on fungal residues compared to bacterial illustrate a distinct community response to warming. We conclude that warming has the potential to influence soil C sequestration through increased microbial residue inputs, consequently altering its composition and source configuration. Our work provides valuable insights at the molecular level to identify mechanisms of microbial-mediated C processes that are influenced by climate change in high elevation ecosystems.