Local linear stability analysis has been shown to provide valuable information about the response of jet diffusion flames to flow-field perturbations. However, this analysis commonly relies on several modelling assumptions about the mean flow prescription, the thermo-viscous-diffusive transport properties, and the complexity and representation of the chemical reaction mechanisms. In this work, the effects of these modelling assumptions on the stability behaviour of a jet diffusion flame are systematically investigated. A flamelet formulation is combined with linear stability theory to fully account for the effects of complex transport properties and the detailed reaction chemistry on the perturbation dynamics. The model is applied to a methane–air jet diffusion flame that was experimentally investigated by Füri et al. (Proc. Combust. Inst., vol. 29, 2002, pp. 1653–1661). Detailed simulations are performed to obtain mean flow quantities, about which the stability analysis is performed. Simulation results show that the growth rate of the inviscid instability mode is insensitive to the representation of the transport properties at low frequencies, and exhibits a stronger dependence on the mean flow representation. The effects of the complexity of the reaction chemistry on the stability behaviour are investigated in the context of an adiabatic jet flame configuration. Comparisons with a detailed chemical-kinetics model show that the use of a one-step chemistry representation in combination with a simplified viscous-diffusive transport model can affect the mean flow representation and heat release location, thereby modifying the instability behaviour. This is attributed to the shift in the flame structure predicted by the one-step chemistry model, and is further exacerbated by the representation of the transport properties. A pinch-point analysis is performed to investigate the stability behaviour; it is shown that the shear-layer instability is convectively unstable, while the outer buoyancy-driven instability mode transitions from absolutely to convectively unstable in the nozzle near field, and this transition point is dependent on the Froude number.