When considering alternative fuels for aviation, factors such as the overall efficiency of the combustion process and the levels of emissions emitted to the atmosphere need to be critically evaluated. The physical and chemical properties of a fuel influence the combustion efficiency and emissions and therefore need to be considered. The energy content of a biofuel, which is influenced negatively by the presence of oxygen in the molecular structure (i.e. oxygenated chemical compounds), is relatively low when compared with that of conventional jet fuel. This means that the overall efficiency of the process will be different. In this article, two possible scenarios have been investigated in order to assess the potential to directly replace conventional jet fuel – kerosene with methyl buthanoate – MB (a short chain fatty acid methyl ester – representing biofuel) and a synthetic jet fuel (Fischer–Tropsch fuel) using computational fluid dynamics (CFD) modelling in a typical modern air-spray combustor. A detailed comparison of kerosene with alternative fuel performance has been made. In addition, the impact of fuel blending on the combustion performance has been investigated. The CFD results indicate that there are notable differences in the engine performance and emissions when replacing conventional jet fuel with alternative fuels. The effect of alternative fuel chemistry on the combustion characteristics is noticeable both in the flamelet calculation and the CFD main flow field computations. This is particularly the case for MB.