Organic biomarker and nannofossil assemblages are used in combination with sedimentary petrology to identify the role of diagenesis for the formation of a rhythmic calcareous succession. A record from the Early Pliocene of the Maldives (Ocean Drilling Program, ODP Leg 115) is presented containing precession and eccentricity cycles expressed as variable aragonite content. Additional sub-Milankovitch cycles are caused by rhythmic precipitation of calcite cement in the lower part of the interval. Comparison with palaeo-productivity indicators (nannofossils, chlorin, total organic carbon) suggests that cementation occurs preferentially in intervals characterized by increasing or decreasing productivity. The coupled variability in productivity and carbonate diagenesis is attributed to the effect of organic matter degradation in the sediment. The observed combination of primary and diagenetic factors hampers the interpretation of the cyclicity on Milankovitch and sub-Milankovitch scales. Diagenetically stable proxies for palaeo-productivity, such as nannofossil assemblage data, were used to distinguish between palaeoclimate and diagenetic influences.