To examine the need to incorporate in situ wettability measurements in direct numerical simulations, we compare waterflooding experiments in a mixed-wet carbonate from a producing reservoir and results of direct multiphase numerical simulations using the color-gradient lattice Boltzmann method. We study the experiments of Alhammadi et al. (Sci Rep 7(1):10753, 2017. https://doi.org/10.1038/s41598-017-10992-w) where the pore-scale distribution of remaining oil was imaged using micro-CT scanning. In the experiment, in situ contact angles were measured using an automated algorithm (AlRatrout et al. in Adv Water Resour 109:158–169, 2017. https://doi.org/10.1016/j.advwatres.2017.07.018), which indicated a mixed-wet state with spatially non-uniform angles. In our simulations, the pore structure was obtained from segmented images of the sample used in the experiment. Furthermore, in situ measured angles were also incorporated into our simulations using our previously developed wetting boundary condition (Akai et al. in Adv Water Resour 116(March):56–66, 2018. https://doi.org/10.1016/j.advwatres.2018.03.014). We designed six simulations with different contact angle assignments based on experimentally measured values. Both a constant contact angle based on the average value of the measured values and non-uniform contact angles informed by the measured values gave a good agreement for fluid pore occupancy between the simulation and the experiment. However, the constant contact angle assignment predicted 54% higher water effective permeability after waterflooding than that estimated for the experimental result, whereas the non-uniform contact angle assignment gave less than 1% relative error. This means that to correctly predict fluid conductivity in mixed-wet rocks, a spatially heterogeneous wettability state needs to be taken into account. The novelty of this work is to provide a direct pore-scale comparison between experiments and simulations employing experimentally measured contact angles, and to demonstrate how to use measured contact angle data to improve the predictability of direct numerical simulation, highlighting the difference between the contact angle required for the simulation of dynamic displacement process and the contact angle measured at equilibrium after waterflooding.