The carbon cycle is a major forcing component in the global climate system. Modelling studies, aiming to ex- plain recent and past climatic changes and to project future ones, increasingly include the interaction between the phys- ical and biogeochemical systems. Their ocean components are generally z-coordinate models that are conceptually easy to use but that employ a vertical coordinate that is alien to the real ocean structure. Here, we present first results from a newly-developed isopycnic carbon cycle model and demon- strate the viability of using an isopycnic physical component for this purpose. As expected, the model represents well the interior ocean transport of biogeochemical tracers and pro- duces realistic tracer distributions. Difficulties in employing a purely isopycnic coordinate lie mainly in the treatment of the surface boundary layer which is often represented by a bulk mixed layer. The most significant adjustments of the ocean biogeochemistry model HAMOCC, for use with an isopycnic coordinate, were in the representation of upper ocean biological production. We present a series of sensi- tivity studies exploring the effect of changes in biogeochem- ical and physical processes on export production and nutrient distribution. Apart from giving us pointers for further model development, they highlight the importance of preformed nu- trient distributions in the Southern Ocean for global nutrient distributions. The sensitivity studies show that iron limitation for biological particle production, the treatment of light pen- etration for biological production, and the role of diapycnal mixing result in significant changes of nutrient distributions and liniting factors of biological production.