Terrestrial environments are highly complex and dynamic. It consists of various types of soils which are constantly exposed to fluctuating conditions affecting their physical and biological properties. Moreover, soils are delivering several ecosystem services with high relevance for the human well-being such as water purification, nutrient cycling, or biodegradation. For many of those ecosystem services, microorganisms are the main drivers. In consequence, it is important to understand the functional response of microbial ecosystems to disturbances. Thus, identifying key factors for the functional stability of microbial ecosystems in terrestrial environments is of high interest. A powerful tool for analysing dynamics and underlying mechanisms of ecosystems are computational simulation models. Within this doctoral thesis, a spatiotemporally explicit bacterial simulation model was developed for assessing dynamics of biodegradation as a typical microbial ecosystem function under the influence of disturbances. Disturbances were introduced as lethal events for the bacteria within a certain, randomly picked disturbance area. The disturbance characteristics vary in the spatial configuration and frequency of the disturbance events. Functional stability was analysed in terms of the ability to recover the function after a single disturbance event, i.e. functional resilience, and the ability to maintain the function during recurrent disturbance events, i.e. functional resistance. Key factors for functional stability were assessed by systematically varying properties and processes of the microbial ecosystem and characteristics of the disturbance regime. Simulation results show a high influence of the disturbance characteristics, especially its spatial distribution pattern, on the stability of biodegradation. Functional resistance and resilience increase with fragmentation of the spatial pattern of the disturbances. The frequency of recurrent disturbance events proved also essential for the functional resistance: if the disturbances occur too often, the emergence of a functional collapse may not be preventable. However, if the fragmentation of the applied disturbance patterns increases, the function is also maintained under more frequent disturbances without a functional collapse. Ecological processes such as bacterial dispersal and growth are shown to enhance the biodegradation performance, but only under specific disturbance regimes, again depending on frequency and fragmentation of the disturbances. Dispersal networks are shown to increase the functional stability in many scenarios and, thus, may serve as a buffer mechanism against disturbances. Therefore, strategies facilitating these ecological processes, for instance stimulating fungi that act as dispersal networks for bacteria, or modulating the physical soil structure to alter the spatial configuration of disturbances are proposed to increase the functional stability of microbial ecosystems.