Six different TiO2/CNT nanocomposite-coated polyvinylidene-fluoride (PVDF) microfilter membranes (including –OH or/and –COOH functionalized CNTs) were evaluated in terms of their performance in filtering oil-in-water emulsions. In the early stages of filtration, until reaching a volume reduction ratio (VRR) of ~1.5, the membranes coated with functionalized CNT-containing composites provided significantly higher fluxes than the non-functionalized ones, proving the beneficial effect of the surface modifications of the CNTs. Additionally, until the end of the filtration experiments (VRR = 5), notable flux enhancements were achieved with both TiO2 (~50%) and TiO2/CNT-coated membranes (up to ~300%), compared to the uncoated membrane. The irreversible filtration resistances of the membranes indicated that both the hydrophilicity and surface charge (zeta potential) played a crucial role in membrane fouling. However, a sharp and significant flux decrease (~90% flux reduction ratio) was observed for all membranes until reaching a VRR of 1.1–1.8, which could be attributed to the chemical composition of the oil. Gas chromatography measurements revealed a lack of hydrocarbon derivatives with polar molecular fractions (which can act as natural emulsifiers), resulting in significant coalescent ability (and less stable emulsion). Therefore, this led to a more compact cake layer formation on the surface of the membranes (compared to a previous study). It was also demonstrated that all membranes had excellent purification efficiency (97–99.8%) regarding the turbidity, but the effectiveness of the chemical oxygen demand reduction was slightly lower, ranging from 93.7% to 98%.