Governments, organisations and individuals have recognised the need to reduce their greenhouse gas (GHG) emissions. To identify where savings can be made, and to monitor progress in reducing emissions, we need methodologies to quantify GHG emissions and sequestration. Through the Australian Government’s Carbon Farming Initiative (CFI) landholders may generate credits for reducing emissions and/or sequestering carbon (C). National GHG inventories for the United Nations Framework Convention on Climate Change, and accounting under the Kyoto Protocol use a sectoral approach. For example, fuel use in agriculture is reported in the transport component of the energy sector; energy use in producing herbicide and fertiliser is included in the manufacturing section of the energy sector; sequestration in farm forestry is reported in the land use, land-use change and forestry sector, while emissions reported in the agriculture sector include methane (CH4) from ruminant livestock, nitrous oxide (N2O) from soils, and non-carbon dioxide (CO2) GHG from stubble and savannah burning. In contrast, project-level accounting for CFI includes land-use change, forestry and agricultural sector emissions, and significant direct inputs such as diesel and electricity. A C footprint calculation uses a life cycle approach, including all the emissions associated with an organisation, activity or product. The C footprint of a food product includes the upstream emissions from manufacturing fertiliser and other inputs, fuel use in farming operations, transport, processing and packaging, distribution to consumers, electricity use in refrigeration and food preparation, and waste disposal. Methods used to estimate emissions range from simple empirical emissions factors, to complex process-based models. Methods developed for inventory and emissions trading must balance the need for sufficient accuracy to give confidence to the market, with practical aspects such as ease and expense of data collection. Requirements for frequent on-ground monitoring and third party verification of soil C or livestock CH4 estimates, for example, may incur costs that would negate the financial benefit of credits earned, and could also generate additional GHG emissions. Research is required to develop practical on-farm measures of CH4 and N2O, and methods to quantify C in environmental plantings, agricultural soils and rangeland ecosystems, to improve models for estimation and prediction of GHG emissions, and enable baseline assessment. There is a need for whole-farm level estimation tools that accommodate regional and management differences in emissions and sequestration to support landholders in managing net emissions from their farming enterprises. These on-farm ‘bottom-up’ accounting tools must align with the ‘top-down’ national account. To facilitate assessment of C footprints for food and fibre products, Australia also needs a comprehensive life cycle inventory database. This paper reviews current methods and approaches used for quantifying GHG emissions for the land-based sectors in the context of emissions reporting, emissions trading and C footprinting, and proposes possible improvements. We emphasise that cost-effective yet credible GHG estimation methods are needed to encourage participation in voluntary offset schemes such as the CFI, and thereby achieve maximum mitigation in the land-based sector.