Understanding the drivers of ecosystem stability has been a key focus of modern ecology as the impacts of the Anthropocene become more prevalent and extreme. Marine Protected Areas (MPAs) are tools used globally to promote biodiversity and mediate anthropogenic impacts. However, assessing the stability of natural ecosystems, and responses to management actions, is inherently challenging due to the complex dynamics of communities with many interdependent taxa. Here we assess whether a MPA network in the Channel Islands, USA creates spatiotemporal heterogeneity in trophic networks, which reduces interaction strength and synchrony among prey, in‐turn promoting temporal stability in community structure of trophic networks at community and metacommunity scales. At the community scale, only trophic networks within MPAs at Santa Rosa Island showed greater temporal stability than reference sites, likely driven by reduced prey synchrony. Across islands, competition was sometimes greater and predation always greater in MPAs compared to reference sites. These increases in interaction strength resulted in lower temporal stability of trophic networks. While MPAs also reduced prey synchrony at the metacommunity scale, this was insufficient to stabilize trophic networks. In contrast, temporal variation in sea surface temperature had strong positive direct effects on stability at the regional scale, and indirect effects at the local scale, through reductions in competition and predation strength. Although MPAs can be effective management strategies for protecting certain species or locations, our findings for this MPA network suggest that temperature variation has a stronger influence on metacommunity temporal stability by mediating species interactions and promoting a mosaic of spatiotemporal variation in community structure of trophic networks. By capturing the full spectrum of environmental variation in network planning, MPAs will have the greatest capacity to promote ecosystem stability in response to climate change.This article is protected by copyright. All rights reserved