The principles of microbial community assembly in engineered ecosystems (particularly biotreatment processes) exposed to high-intensity environmental disturbances remain poorly understood. In this study, we conducted a meta-analysis of microbial communities across nine datasets from bioreactors operated under varied conditions. Null model-based analysis indicated that stochastic processes predominantly govern community assembly during contaminant-free selection phases or stable operation. In contrast, deterministic processes consistently govern initial acclimation of activated sludge. These processes then shift toward stochastic dominance as the operation stabilizes. The presence of environmental disturbances—such as shock, refeeding, or stress—during operation increases the relative contribution of deterministic processes to community structuring. Notably, low bioreactor performance is associated with deterministic assembly, whereas sustained stable operation corresponds to stochastic dynamics, irrespective of reactor type or condition. These findings were integrated across four categories of biotreatment operations to illustrate how specific disturbances influence microbial community succession and performance stability. This work advances the theoretical understanding of microbial dynamics in engineered systems and offers practical insights into linking community assembly mechanisms with bioreactor function.