Catastrophic state changes often occur in ecosystems as consequences of shifts in the dominant life forms, such as in the case of sportfish introduction into naturally fishless mountain lakes. While the pronounced ecological displacement of native communities by these novel predators (i.e., weak resistance) is well documented, few studies have also examined the dynamics of their recovery rates (i.e., “engineering resilience”) following stressor removal. We addressed this knowledge gap by quantifying the taxonomic and species trait‐based ordination trajectories of crustacean zooplankton communities in stocked alpine lakes, which differed in how they were restored to a natural fishless state over a period of six decades. Resilience and resistance trajectories differed in each lake as the ecological importance of trait‐based species recolonization potential (e.g., asexual vs. sexual reproduction) replaced that of tolerance of size‐selective predation by fish (e.g., body size, pigmentation, motility). As a result, re‐establishment of large‐bodied zooplankton following the elimination of fish restored annual secondary production. In contrast, a more gradual unidirectional ordination trajectory toward smaller zooplankton body size and a decline in total zooplankton biomass occurred in a nearby alpine lake containing a protected native bull trout population. Although recovery trajectories returned via routes that differed from those of earlier resistance trajectories (i.e., hysteresis), we discovered that full taxonomic and functional recovery was realized in all the restored fishless lakes within three decades, regardless of the approach used to achieve ecosystem restoration.