1. Prairie dogs (Cynomys sp.) are considered keystone species and ecosystem engineers for their grazing and burrowing activities (summarized here as disturbances). As climate changes and its variability increases, the mechanisms underlying organisms’ interactions with their habitat will likely shift. Understanding the mediating role of prairie dog disturbance on vegetation structure, and its interaction with environmental conditions through time, will increase knowledge on the risks and vulnerability of grasslands. 2. Here, we compared how plant taxonomic and functional diversity metrics, along with community-weighted trait means (CWM), respond to prairie dog disturbance across grassland types and seasons in a conservation priority, semiarid grassland of Northeast Mexico. 3. Our findings suggest that functional metrics and CWM analyses responded to interactions between prairie dog disturbance, grassland type and season, whilst species diversity and cover measures were less sensitive to the role of prairie dog disturbance. Contrary to previous studies, we found weak evidence that prairie dog disturbance has a negative effect on vegetation structure, except for minimal effects on C4 and graminoid cover, which depend mainly on season. Grassland type and season explained most of the effects on plant functional and taxonomic diversity as well as CWM traits. Furthermore, we found that leaf area as well as forb and annual cover increased during the wet season, independent of prairie dog disturbance. 4. Our results provide evidence that prairie dog disturbance is less important than grassland type and that environmental effects have a stronger role than grazing and animal disturbances on vegetation. We argue that a focus on disturbance and grazing effects is misleading, and instead attention is needed on the relationships between vegetation and environmental conditions which will be critical to understand semi-arid grassland dynamics in the region. In addition, explicit management strategies to mitigate climate change would need to consider these relationships