Traditional conservation practices have primarily relied on maintaining biodiversity by preserving species and habitats in place. Many regions are experiencing unprecedented environmental conditions, shifts in species distribution and habitats, and high turnover in species composition, resulting in ecological transformation. Natural resource managers have lacked tools for identifying and selecting strategies to manage ecosystem transformation. A recently formalized decision support framework provides a way for managers to resist, accept, or direct (RAD) the trajectory of change. We begin by identifying how historical conservation practices are built into the RAD framework. Next, we describe how RAD can be used to implement climate change adaptation actions, using examples from the Mojave Desert to provide ecological context. Third, we discuss how the RAD framework can assist with the creation of conservation portfolios, facilitating the maintenance of overall biodiversity across a landscape. Preserving species assemblages in their current state, or restoring them to historical conditions, will not always be possible, and RAD allows for explicit deliberation about when and where to prioritize scarce resources. We conclude with a set of guidelines for conservation practitioners or managers moving forward. Although operating under an increasingly uncertain future is daunting, managers can utilize RAD to conserve biodiversity and effectively handle ecosystem transformation.