Abstract Mesophotic coral ecosystems (30–150 m depth) present a high oceanic biodiversity, but remain one of the most understudied reef habitats, especially below 60 m depth. Here, we have assessed the rates of photosynthesis and dissolved inorganic carbon (DIC) and nitrogen (DIN) assimilation by Symbiodiniaceae associated with four soft coral species of the genus Sinularia and two stony coral species of the genus Leptoseris collected respectively at 65 and 80–90 m depth in the Gulf of Eilat. Our study demonstrates that both Leptoseris and Sinularia species have limited autotrophic capacities at mid‐lower mesophotic depths. DIC and DIN assimilation rates were overall ~ 10 times lower compared to shallow corals from 10 m depth in the same reef. While Leptoseris symbionts transferred at least 50% of the acquired nitrogen to their host after 8‐h incubation, most of the nitrogen was retained in the symbionts of Sinularia . In addition, the host tissue of Sinularia species presented a very high structural carbon to nitrogen ratio (C : N) compared to Leptoseris or to the shallow coral species, suggesting nitrogen limitation in these mesophotic soft corals. The limited capacity of soft coral symbionts to acquire DIN and transfer it to the coral animal, as well as the high C : N ratios, might explain the scarcity of symbiotic soft corals at mid‐lower mesophotic depths compared to their prevalence in the shallower reef. Overall, this study highlights the significance of DIN for the distribution of the Cnidarian‐ Symbiodiniaceae association at mesophotic depth.