Any fishery management scheme, such as individual fishing quotas (IFQs) or marine protected areas, should be designed to be robust to potential shifts in the biophysical system. Here we couple possible catch scenarios under an IFQ scheme with ocean acidification impacts on shelled benthos and plankton, using an Atlantis ecosystem model for the US West Coast. IFQ harvest scenarios alone, in most cases, did not have strong impacts on the food web, beyond the direct effects on harvested species. However, when we added the impacts of ocean acidification, the abundance of commercially important groundfish such as English sole (Pleuronectes vetulus), arrowtooth flounder (Atheresthes stomias), and yellowtail rockfish (Sebastes flavidus) declined up to 20%–80%, owing to the loss of shelled prey items from their diet. English sole exhibited a 10-fold decline in potential catch and economic yield when confronted with strong acidification impacts on shelled benthos. Therefore, it seems prudent to complement IFQs with careful consideration of potential global change effects such as acidification. Our analysis provides an example of how new ecosystem modeling tools that evaluate cumulative impacts can be integrated with established management reference points and decision mechanisms.