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Conservation and management of kakapo (Strigops habroptilus) has spanned more than a century and has cost many millions of dollars. Government policy goals have supported these efforts throughout this long period but decisions made have not always reflected an optimal approach to achieving them. Decisions made have influenced not only whether kakapo will recover, but also the time span to recovery and its cost, which have impacted on the ability to meet broader biodiversity goals. The establishment, in 1987, of a single conservation agency, administering both the land and the species contained thereon, significantly changed the way biodiversity management was delivered in New Zealand and created enormous potential for integrated conservation outcomes. Despite this, decision-making for managers of threatened species conservation programmes has become more complex as an increasing number of endangered species compete for limited resources. Using kakapo as an example, historic and recent recovery decisions are evaluated and the need for a decision-making framework to improve threatened species recovery and overall biodiversity maintenance is discussed.