Antarctic terrestrial biodiversity is challenged by rapid climatic changes and expansion of the human footprint. As well as the potential for environmental damage at the local level, these challenges are likely to act synergistically to increase the risk of introduction and establishment of non-native species and diseases and reduce the resilience of native ecosystems. The Protocol on Environmental Protection to the Antarctic Treaty (‘the Protocol’) entered into force in 1998 and is the main governance mechanism that regulates environmental management in Antarctica. We examine how well the Protocol and associated management tools are currently equipped to protect Antarctic terrestrial biodiversity in a warmer and busier Antarctic, considering likely future challenges, current levels of compliance with the Protocol and implementation of its requirements, and participation in environmental matters by Antarctic Treaty Parties. We argue that a strategic-level response will be needed to boost the ability of the Antarctic Treaty System to deal with the large-scale, pervasive challenges of climate change and increased human activity. A strategic planning approach that can (1) account for trends over long periods, (2) take into consideration cumulative effects, (3) be guided by a set of consciously chosen priorities, and (4) take an integrated approach towards management of human activities and the conservation of the Antarctic environment, will permit the anticipation of upcoming challenges and risks and adoption of proactive and holistic management strategies.