During revegetation, the maintenance of soil carbon (C) pools and nitrogen (N) availability is considered essential for soil fertility and this study aimed to evaluate contrasting methods of site preparation (herbicide and scalping) with respect to the effects on soil organic matter (SOM) during the critical early establishment phase. Soil total C (TC), total N (TN), hot-water extractable organic C (HWEOC), hot-water extractable total N (HWETN), microbial biomass C and N (MBC and MBN), total inorganic N (TIN) and potentially mineralizable N (PMN) were measured over 53 weeks. MBC and MBN were the only variables affected by herbicide application. Scalping caused an immediate reduction in all variables, and the values remained low without any sign of recovery for the period of the study. The impact of scalping on HWETN and TIN lasted 22 weeks and stabilised afterwards. MBC and MBN were affected by both herbicide and scalping after initial treatment application and remained lower than control during the period of the study but did not decrease over time. While scalping had an inevitable impact on all soil properties that were measured, that impact did not worsen over time, and actually improved plant growth (unpublished data) while reducing site establishment costs. Therefore, it provides a useful alternative for weed control in revegetation projects where it is applied only once at site establishment and where SOM would be expected to recover as canopy closure is obtained and nutrient cycling through litterfall commences.