The study explores a novel proxy for reconstructing atmospheric CO2 concentrations during the Late Devonian–Mississippian, a key interval marked by the transition from a greenhouse to an icehouse climate and the onset of the Late Palaeozoic Ice Age. Traditional proxies for Palaeozoic CO2 levels, such as palaeosols and vascular plant and phytoplankton remains, are limited by scarcity, poor dating, or susceptibility to diagenetic alteration. To address these challenges, this work evaluates the decoupled carbon isotope composition of conodont elements and host carbonates. Based on integrated isotope analyses and comparison with compiled CO2 estimates, the study reveals a significant negative correlation between the decoupling of carbon isotope composition of conodont elements and host carbonates and atmospheric CO2 content. The results indicate taxon-specific trends, with Ozarkodinida and Prioniodinida exhibiting similar regression gradients but distinct intercepts, suggesting ecological or physiological influences on isotopic fractionation. The findings support the potential of the decoupling of carbon isotope composition of conodont elements and host carbonates as a potential proxy for atmospheric CO2, with implications for reconstructing spatial and temporal variations in Palaeozoic carbon cycles and climate dynamics.