Rapid melting of the Western Antarctic Peninsula (WAP) glaciers is a compelling piece of evidence of how climate change affects our planet. This study investigated the impact of global warming-facilitated environmental change on microbial community structure and function by subjecting sediments sampled near the Fourcade Glacier in Potter Cove, WAP, to a temperature gradient and supply of metabolic nutrients relevant for the fate of carbon in marine ecosystems. We found that (i) temperature as a key environmental change driver will significantly impact microbial community structure, but ecological functions supported by fresh supply of nutrients from glacial meltwater will prevail; (ii) keystone species responsible for specialized functions are metabolically flexible, persisting from 2°C to 25°C; and (iii) in addition to keystone species, global warming will activate certain hitherto inactive but endogenous microorganisms in response to either changes in temperature or nutrient flux to sustain ecosystem functions. Our study presents evidence of sediment microbiome resilience in response to strong temperature or nutrient flux shifts, thereby adding another layer of evidence of nature’s adaptability to global warming.