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The global protected area (PA) system has a key role to play in biological conservation, and it is thus vital to understand the factors that are likely to limit this potential. Attention to date has focused foremost on the consequences of biases in the spatial distribution of PAs for their effectiveness and efficiency in representing biodiversity. What is less clear is the extent to which these biases may also have affected the likelihood with which PAs coincide with or are influenced by particular kinds of threatening processes, further undermining their role. An obvious candidate for such concerns is metal mining activities. Here we demonstrate that approximately 7% of mines for four key metals directly overlap with PAs and a further 27% lie within 10 km of a PA boundary. Moreover, those PAs with mining activity within their boundaries constitute around 6% of the total areal coverage of the global terrestrial PA system, and those with mining activity within or up to 10 km from their boundary constitute nearly 14% of the total area. Given the distances over which mining activities can have influences, the persistence of their effects (often long after actual operations have closed down), and the rapidly growing demand for metals, there is an urgent need to limit or mitigate such conflicts.