Fishing-induced biomass depletion is common on coral reefs. Yet, fisheries persist, maintaining the livelihoods of millions of fishers. Understanding this persistence is key to sustained reef fisheries in a time of global changes. Here we combine snapshot fish surveys and individual models of growth and mortality in a novel framework to evaluate potential reef fisheries productivity across a whole Pacific country (Tonga) spanning a major fishing pressure gradient. We provide empirical evidence of compensatory ecological responses triggered by fishing on coral reefs. High fishing exploitation drove biomass declines, yet, for a given exploitation level, productivity was consistently larger than expected from the remaining biomass. This buffering response provided, on average, an extra ~20% or 0.24 kg ha−1 d−1 of target fish production—a sizeable proportion of reported coral reef fisheries yields. Such ‘buffering productivity’ was strongest in wave-exposed, shallower, benthic-diverse and structurally complex areas. Consequently, a reef’s capacity to deliver these responses is conditional on where it is located (that is, some habitats have higher propensity to support strong responses) and on its disturbance history (for example, episodic coral mortality that reduces structural complexity and benthic diversity). Thus, while compensatory buffering production may help explain persistent yields in biomass-depleted coral reef fisheries, the sustainability of these yields may be jeopardized by the impacts of climate change.