Fisheries management has focused on single stocks, not directly accounting for species interactions, and usually only considering economic factors in post hoc analysis. This approach has been successfully applied for many species over many years, but may also inadvertently result in greater risks being incurred. We demonstrate a portfolio optimization approach to inform a broader set of fishery concerns as a way to emphasize species interactions and economic considerations in resource management decision making. The approach can use readily available data on landings and revenue to generate easily digestible indicators of risk, namely the risk gap (i.e., the difference between actual and optimal portfolio values). Herein, we calculate portfolio efficiency frontiers that minimize risk for target revenue outcomes and resulting risk gaps for commercial fisheries using the top 25 landed‐value species in six U.S. fisheries regions. Most regions exhibited a risk gap on the order of US$20–50 million, collectively on average over $250 million. Risk gaps can be used as ecosystem‐level indicators to inform managers of the unnecessary risk being assumed for a given level of revenue for a portfolio of fisheries stocks, which can move us towards operational ecosystem‐based fisheries management.