Large-eddy simulations (LES) of a jet issuing into a hot and diluted coflow are performed. To model this three-stream burner configuration, which is operated in the moderate and intense low-oxygen dilution (MILD) combustion regime, a flamelet/progress variable (FPV) formulation is extended by introducing an additional conserved scalar. This additional scalar is associated with the oxidizer split, and is used to identify flamelets of different mixture composition. Due to the extended spatial structure of this jet diffusion flame, the moderate Reynolds number, and the overall lean operating condition, different flamelets interact only weakly in mixture composition space, so that the thermochemical state-space is populated from the solution of the one-dimensional flamelet equations. To account for the turbulence/chemistry interaction on numerically unresolved scales, a presumed probability density function (PDF) is used in the LES combustion model. This three-stream FPV combustion model is applied in LES of the MILD combustor, which was experimentally investigated by Dally et al. (2002) [4]. The comparison with results obtained from the single-mixture fraction FPV formulation shows that the coflow mixture composition can only inadequately be represented by a single mixture fraction, resulting in a significant overprediction of the flame temperature and CO mass fraction. The second part of this work addresses the sensitivity of the flow field and flame structure to the specification of scalar inflow conditions under kinetics-controlled, low-Damköhler number combustion conditions. To this end, LES calculations are performed that employ an increasing level of fidelity in the specification of the scalar boundary conditions, including homogeneous and intermittent turbulent scalar inflow conditions that are derived from experimental data. From this analysis, it is shown that the consideration of turbulent fluctuations in the scalar composition leads to improved predictions for temperature and mass fractions of CO and OH. Furthermore, the results from this simulation also suggest that effects of scalar inflow conditions are not only confined to the nozzle-near region but extend throughout the entire flame. It is anticipated that these findings could also be of relevance to other simulations of kinetics-controlled and low-temperature combustion systems, including autoignition, lifted flames, and premixed systems in which flames are stabilized by vitiated and hot coflows.