Cold-water corals (CWC) have long been considered particularly sensitive to ocean acidification (OA). However, a number of laboratory studies indicate that exposure to acidic waters does not affect CWC growth but in situ OA studies on CWC are scarce. In the naturally acidified Comau Fjord (Chile), high densities of the cosmopolitan CWC Desmophyllum dianthus are found at or below aragonite saturation (Ωar ≤ 1), but it is not known if the corals’ ability to up-regulate the pH in the calcifying fluid (pHcf) and calcify shows seasonal fluctuations due to changes in Ωar and/or food supply. In the present study, corals were sampled along both horizontal and vertical pH gradients in Comau Fjord (equivalent to 0.81 < Ωar < 1.45 and 0.65 < Ωar < 1.45, respectively). We compared D. dianthus’ calcification rates (alkalinity anomaly technique), skeletal carbonate accretion (buoyant weight technique, BWT), linear extension rates (fluorescent microscopy) and pHcf (skeletal δ11B; LA-ICP-MS) with the physico-chemical conditions in the water column (T, Ωar) in austral summer 2016/2017 and winter 2017. Growth rates (BWT) were higher in summer than in winter, with highest values, irritably, at Ωar < 1. Cross-transplant experiments showed that D. dianthus is able to acclimatise to Ωar < 1. A strong biological pHcf up-regulation of 1.13 pH units was found at low pHT with δ11B of 25.6 ‰ compared to ΔpH of 0.77 (δ11B = 23.4 ‰) at higher pHT. The present study shows that Ωar alone is a poor predictor of D. dianthus’ pH up-regulation and growth. They suggest a complex combination of biological and physical factors that need to be considered to constrain the future of CWC in an era of OA.