Land managers must balance the needs of a variety of species when manipulating habitats. Structured decision making provides a systematic means of defining choices and choosing among alternative management options; implementation of a structured decision requires quantitative approaches to predicting consequences of management on the relevant species. Multi-species occupancy models provide a convenient framework for making structured decisions when the management objective is focused on a collection of species. These models use replicate survey data that are often collected on managed lands. Occupancy can be modeled for each species as a function of habitat and other environmental features, and Bayesian methods allow for estimation and prediction of collective responses of groups of species to alternative scenarios of habitat management. We provide an example of this approach using data from breeding bird surveys conducted in 2008 at the Patuxent Research Refuge in Laurel, Maryland, evaluating the effects of eliminating meadow and wetland habitats on scrub-successional and woodland-breeding bird species using summed total occupancy of species as an objective function. Removal of meadows and wetlands decreased value of an objective function based on scrub-successional species by 23.3% (95% CI: 20.3–26.5), but caused only a 2% (0.5, 3.5) increase in value of an objective function based on woodland species, documenting differential effects of elimination of meadows and wetlands on these groups of breeding birds. This approach provides a useful quantitative tool for managers interested in structured decision making.