We present a first species-specific evaluation of marine core-top dinoflagellate cyst carbon isotope fractionation (ε_p) to assess natural pCO₂ dependency on ε_p and explore its geological deep-time paleo-pCO₂ proxy potential. We find that ε_p differs between genera and species and that in Operculodinium centrocarpum, ε_p is controlled by pCO₂ and nutrients. Our results highlight the added value of δ¹³C analyses of individual micrometer-scale sedimentary organic carbon particles.