Australian agricultural soils have sustained a substantial loss of naturally low levels of soil organic carbon (SOC) through conversion of native vegetation to cropping. Recently, government programmes focused on greenhouse gas emission abatement have provided incentives for conversion of cropland to permanent pastures. Concurrently, some farmers are pursuing innovative pasture grazing practices, such as the use of perennial pastures and rotational grazing. Although gaining carbon credits is generally not the main driver for uptake of these practices, there is significant potential for soil carbon sequestration. We investigated SOC stocks across a chronosequence of pastures sown with temperate, perennial grasses in south-western Australia. This study presents a rare insight into short- and long-term carbon dynamics in a novel agricultural system, which has potential for greater uptake within this region. SOC stocks for the upper 30 cm of soil ranged from 64.9 t ha−1 in the longest established pasture (sown in 2003 and sampled in 2012 and 2014) to 25.2 t ha−1 in a poorly performing pasture (sown in 2007). SOC stocks at two of the sampled sites showed large (19.7 to 22.0 t ha−1) fluctuations over a 2-year period, which was likely linked to targeted management practices intended to increase pasture productivity. Taking into account farmers' needs for experimenting with management practices and their detailed local knowledge of why certain locations responded in different ways is paramount for developing longer term and larger scale approaches to improve soil health through novel agricultural practices.