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Abstract Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long‐term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.