Global change exposes ecosystems to changes in the frequency, magnitude and concomitancy of disturbances, which impact the composition and functioning. Here we experimentally evaluate effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The resistance, resilience and functional stability of these communities is critically important for water quality, productivity and consequently ecosystem services, such as fishery yields. Yet, little is known about the underlying traits. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. To study the impact of pulsed disturbances on community assembly and functioning in dependence of metabolic costs, we performed a 41-days pulse disturbance experiment crossed with two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability dependent patterns of superordinate community structural patterns and functioning, such as genomic trait distributions, species diversity, and functional resistance in response to disturbances. Genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings thereby mark an important step towards unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience. This has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.