The isolation of specific grain size classes of lithogenic samples and biogenic carbonate from the <63 µm fraction (i.e. clay and silt) of marine sediment is often a prerequisite to further pre-treatments and/or analytical measurements for palaeoceanographic studies. Established techniques employed have included sieving, settling and micro-filtration (and/or a combination of these). However, these methods often use significant amounts of bulk sediment (often up to ∼3 g) and/or require considerable amounts of time during sediment processing (ranging from 48 h to 3 weeks) to isolate a size specific class for further analyses. Here, we build on previous approaches to isolate three grain size classes (e.g. <2 µm, clay; 2–10 µm, fine silt; and 10–63 µm, coarse silt) from the <63 µm fraction of marine sediment with the aid of a centrifuge at varying revolutions per minute using Stokes’ Law. We show the utility of our approach using two common sediment types dominated by (i) lithogenic and (ii) biogenic carbonate (specifically coccoliths) components of marine sediment cores. Our method reduces the amount of sample material required to 1–2 g to provide an isolated clay fraction (or other targeted size fraction) and decreases the sample processing time (to ∼1 hour) to enable high throughput of analysis, when compared to previous techniques for palaeoceanographic proxy measurements.