The compositions and properties of oil-in-water emulsions encountered in industry or the environment vary widely in the nature of surfactants that stabilize them, which poses challenges for applications of membrane separation. Electrospun fiber membranes have shown high permeability and improved robustness against fouling in emulsion separation, but the interaction between emulsions and the membrane, and the fouling mechanism, remains unclear. In this work, electrospun polyamide membranes were challenged by model emulsions of dodecane stabilized by anionic, cationic, non-ionic and zwitterionic surfactants in both dead-end and cross-flow filtration configurations under constant pressure. Analysis of permeate flux and oil rejection revealed that the types of surfactants influenced the membrane fouling in both dead-end and cross-flow systems but in different ways. Fouling in dead-end filtration was found to be a function of the electrostatic interactions between the oil droplets and the membrane, while fouling in cross-flow filtration was mainly determined by the hydrophilic/hydrophobic interactions due to the adsorption of surfactants at the interfaces. Blocking filtration models are used to corroborate these findings and illustrate the transition between modes of fouling in dead-end filtration. A de-fouling process was found in dead-end configuration when separating emulsions stabilized by cationic surfactant, which was attributed to coalescence of oil droplets at the membrane surface, based on the kinetic model and direct observation. These results indicate that not only membrane-foulant but foulant-foulant interactions can influence the membrane fouling. In order to enhance the separation performance, surface modification on the electrospun polyamide membranes were applied by using plasma treatment and layer-by-layer polyelectrolyte deposition. The permeate fluxes of modified membranes were shown to improve when challenged by emulsions stabilized by anionic and cationic surfactants while retaining the oil rejection.