It is open whether El Niño–Southern Oscillation (ENSO) varies under climate change and how potential changes in the marine system are detectable. Here, differences in the influence of ENSO on biogeochemical tracers, pH, productivity, and ocean temperature are analyzed in a continuous 850–2100 CE simulation with the Community Earth System Model. The modeled variance in ENSO amplitude is significantly higher during the Maunder Minimum cold than during the 21st century warm period. ENSO-driven anomalies in global air-sea CO2 flux and marine productivity are two to three times lower and ocean tracer anomalies are generally weaker in the 21st century. Significant changes are detectable in both surface and subsurface waters and are earlier verifiable and more widespread for carbon cycle tracers than for temperature. This suggests that multi-tracer observations of both physical and biogeochemical variables would enable an earlier detection of potential changes in marine ENSO responses than temperature-only data.