The conventional observables to identify a habitable or inhabited environment in exoplanets, such as an ocean glint or abundant atmospheric O₂, will be challenging to detect with present or upcoming observatories. Here we suggest a new signature. A low carbon abundance in the atmosphere of a temperate rocky planet, relative to other planets of the same system, traces the presence of a substantial amount of liquid water, plate tectonics and/or biomass. Here we show that JWST can already perform such a search in some selected systems such as TRAPPIST-1 via the CO₂ band at 4.3 μm, which falls in a spectral sweet spot where the overall noise budget and the effect of cloud and/or hazes are optimal. We propose a three-step strategy for transiting exoplanets: detection of an atmosphere around temperate terrestrial planets in about 10 transits for the most favourable systems; assessment of atmospheric carbon depletion in about 40 transits; and measurements of O₃ abundance to disentangle between a water- versus biomass-supported carbon depletion in about 100 transits. The concept of carbon depletion as a signature for habitability is also applicable for next-generation direct-imaging telescopes.