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Abstract Given the severe implications of climate change and ocean acidification (OA) for marine ecosystems, there is an urgent need to quantify ecosystem function in present‐day conditions to determine the impacts of future changes in environmental conditions. For tropical coral reefs that are acutely threatened by these effects, the metabolism of benthic communities provides several metrics suitable for this purpose, but the application of infrastructure to manipulate conditions and measure community responses is not fully realized. To date, most studies of the effects of OA on coral reefs have been conducted ex situ, and while greater ecological relevance can be achieved through free ocean carbon enrichment (FOCE) experiments on undisturbed areas of reef, such approaches have been deterred by technical challenges (e.g., spatial scale and duration, stable maintenance of conditions). In this study, we describe novel experimental infrastructure called shallow coral reef (SCoRe) FOCE to overcome these challenges and present data from a proof of concept application in Mo'orea, French Polynesia. Our objectives were to (1) implement an autonomous system that could be deployed kilometers from shore, (2) regulate the chemical (pCO₂) and physical properties of seawater over undisturbed, shallow (∼2–5‐m depth) coral reef over multiple weeks, and (3) measure the metabolic response of the coral community to the treatment conditions. We describe the design, function, and application of the SCoRe FOCE, and present data demonstrating its efficacy. This infrastructure has great potential for advancing ecologically relevant studies of the effects of changing environmental conditions on coral reefs.