Microchannel emulsification requires large amounts of surfactant to prevent coalescence and improve emulsions lifetime. However, most numerical studies have considered surfactant-free mixtures as models for droplet formation in microchannels, without taking into account the distribution of surfactant on the droplet surface. In this paper, we investigate the effects of nonuniform surfactant coverage on the microfluidic flow pattern using an extended lattice-Boltzmann model. This numerical study, supported by micro-particle image velocimetry experiments, reveals the likelihood of uneven distribution of surfactant during the droplet formation and the appearance of a stagnant cap. The Marangoni effect affects the droplet breakup by increasing the shear rate. According to our results, surfactant-free and surfactant-rich droplet formation processes are qualitatively different, such that both the capillary number and the Damköhler number should be considered when modeling the droplet generation in microfluidic devices. The limitations of traditional volume and pressure estimation methods for determining the dynamic interfacial tension are also discussed on the basis of the simulation results.